These are my personal opinions for handling confusing, odd, or missing parts of the matrix/software rules.

1: Direct Links and Noise
If you have a direct link between two devices, and have at least 2 marks on the connected devices (ownership is the equivalent of 4), you may use the higher of the direct linked device's ratings for the purposes of overcoming noise. This extends to all the direct linked devices. Changing your Wireless device to use another device for it's matrix link is a free action. If that connection is broken, it defaults back to it's own wireless antenna immediately. Devices used for matrix connections do not need to be hacked in sequence, as they each appear on the matrix as their own icons.
For example: A Street Samurai with a Device Rating 5 commlink implanted could use that link for connecting to the matrix for all his implanted gear, likely increasing their ability to deal with signal noise. Additionally, if the Street Samurai has a Datajack, he could plug it into his Ingram Smartgun X to improve it's connection. Despite all this gear being connected through the commlink, an enemy Decker would still be able to directly attack any matrix connected device without necessarily compromising the commlink first, although normal PAN rules would apply.

Reasoning: Noise, especially jamming, is a potential problem for many characters that use wireless connected devices, like smartlinked guns. Most devices characters use have a rating of 2 or 3, which is easily overwhelmed in spam zones with almost no recourse for characters. Allowing characters to use their commlink, already the central node of their PAN, to boost their signal if directly connected just makes sense to me, and it makes a valid reason why characters with lots of cyberware would want to implant their link, or at least take a datajack to connect to their link.

2: Public and Cross Grid Penalties as Noise
Instead of a -2 penalty for all matrix actions when connected to the Public Grid, being connected via the public grid counts as having 2 points of spam/static zone Noise, thanks to the spotty connection and increased advertising. Similarly, the penalty for working across a grid becomes a stattic/spam Noise 2 instead of a flat -2. Ignore all the rules about cross grid and public grid penalties applying in some sitautiosn and not others. As Noise, the apply unless compensated for with Noise Cancelation. Host systems continue to have no physical location, and thus no distance Noise.

Reasoning: Firstly, I find it a little bit odd that for many devices, it's actually safer to have them on the public grid instead of a local or global one. A Street Samurai's gun is safer on the public grid because it suffers not at all from the -2 matrix action penalty, but anyone trying to hack the device will need to take that penalty or a cross grid penalty. Replacing the generic -2 penalty with noise means the street samurai does potentially suffer from it's effect. Most gear has a device rating of 2, so it would only take an additional noise rating of 1 (downtown, abandoned building) for the device with public grid noise 2 to loose their matrix connection completely. It also provides little protection from hackers, as the noise hinders your connection to the matrix, but as long as you are connected, it doesn't hinder others in interacting with you because noise is always calculated in local spam/static + distance noise. The local noise for the target doesn't mater as long as they are connected. Secondly: The description of the Public grid, with its bandwidth issues, sounds like noise more than a situation requiring a special penalty that applies differently from all other penalties. (Example: Cross grid penalties don't apply inside hosts, but public grid does... a needless complexity.) Thirdly: The set of rules defining when cross grid or public grid penalties applied and didn't apply was needlessly complex, especially when the existing Noise rules handled things fine.
This house rule would be a bit harsh on it's own toward street samurai type characters, but when combined with a few of the other house rules here, like connecting devices to get a better matrix connection, letting commlinks run signal scrubber, and a price to have access to the Local grid, it becomes much less game breaking.

3: Cyberprogram Tweaks
Programs are no longer separated between Cyberdeck and Rigger versions of the program. Additionally, Commlinks are able to run any of the Common Cyberprograms, but not the Hacking Programs. Commlinks can run a number of programs equal to half their device rating, rounded down. Rigger Control Consoles use their Sharing rating for program capacity in general, but only Autosofts are explicitly shared with drones.

Reasoning: It was unclear to me why some cyberprograms were legal/common if the only thing able to run them was the essentially (quasi)illegal cyberdeck. My house rule makes only Browse, Configuration, Edit, Encryption, Signal Scrub, Toolbox, and Virtual Machine available to average users. I see no real harm in allowing average people access to programs like "browse" or "edit" which is essentially letting them have a browser, word processor, or painting program. RCCs and Drones were already able to use cyberprograms, but for some reason they had to use their own version of the software. A cyberdeck version of encryption wouldn't work on an RCC? Seems like needless complexity with little game improvement to me. Lastly, it's not explicitly spelled out that RCCs use their sharing rating as capacity for programs. It could be argued that they get their device rating, but the sharing capacity is simply the subset shared with drones, or even bonus program slots. My house rule removes that ambiguity.

4: Detecting Hidden Icons
"If you know at least one feature of an icon running silent, you can spot the icon (Running Silent, below)" on page 235's list of uses for matrix perception is interpreted to mean that if you know at least 1 feature of an icon you think is running in silent mode on grid or in a host you occupy, you may attempt to directly spot that icon instead of first attempting to determine the presence and number of hidden icons, and then picking randomly among them. The more details you have on a target, the more broadly you can define your search, so you don't need to know the exact make and model of a gun to locate it's icon if you know it's approximate location. If you search broadly, your GM will randomly pick among the applicable options: So looking for a hidden gun icon within 100 meters will get you a random gun running silent, which may or may not be the one the ganger has. Similarly, looking for the wrong thing automatically fails. Note: the Wrapper cyberprogram does not effect the direct targeting of icons. Just because your gun's icon looks like commlink doesn't mean "gun" isn't a feature of the device anymore. Wrapper is useful for running devices in public, not silent.
Valid Examples: "That gun that ganger over there is shooting at me with" or "The Payroll database."
Example of picking wrong: Attempting to locate Wired Reflexes when a character is using Reaction Enhancers.

Reasoning: This is more of a clarification of one way of interpreting the written rules. The tactic of using a lot of stealth RFID tags to keep deckers guessing doesn't exactly seem like it would make the game very fun if it was regularly used. This particular interpretation keeps the tactic from being especially useful at keeping a hacker from directly targeting what they want, although it retains it's usefulness in keeping a hacker guessing if they are just poking around unsure as to what they are looking for.

5: Missing Prices
Local Grid access tends to cost about $200 for a week or $500 per month, but is included in the Middle Lifestyle for your home region. Traveling outside that coverage area will put you on the public grid unless you buy more access. Global Grid access tends to cost $400 for a week or $1000 per month, but one gird is included in the High Lifestyle. At Luxury Lifestyle you can access all the grids.

Autosofts cost $500 per ratting, and have an availability of Rating X 2. Pilot Programs cost the same as Agent software with the same availability.

Note: These are temporary guesses at prices until the real prices are announced. Gird Access prices will apparently be in a future book, but I'm shocked that the prices for Autosofts and Pilot programs were not only left out of the book, but that no one in the know has mentioned what prices were supposed to be included. It's a bit difficult to play a rigger without this information.
The Matrix Connection prices I've picked are %10 of the associated lifestyle where you would normally have access to the grid per month, and I've made a weekly price that less expensive for 2 weeks, but not 3. For the Pilot programs I'm just using Agents, and for Autosofts I'm using half that, which makes them double a Hacking Cyberprogram. It feels right, but I wouldn't be shocked if the real prices end up being a lot more or less. Edit: Autosofts are in the "Hot Fix" errata for missions. I've adjusted this to match.

6: Base CyberDeck
The following cyberdeck is added to the list of options on page 227/439:

"Cobbled Together Links and Electronics," Device Rating 1, Attribute Array 3 2 2 1, Programs: 1, Availability: 2R, Cost: $20,000

Reasoning: The lack of a low end "starter" deck is a bit of continuity issue for the setting. Adding a cheap deck, which like the lowest quality RCC is described as a bunch of legal bits cobbled together into a device, helps described and fill in how deckers get started, and may lend some aid to "Street Level" games.

7: PAN Clarifications
Only a Cyberdeck, Commlink, or RCC can be a Master in a PAN. A device set to be a Master can not also be a Slave to another device in a PAN. A device used to create a Persona on the Matrix does not function as a slave while the Persona is active, but it can still function as a Master.

Reasoning: The rules on forming PANs are unclear on a lot of these topics, and depending on interpretation, odd combinations like daisy chaining links into a deck or using a cheaper link's high device rating for defense on a deck become possible. I think these house rules set the intended use of the PAN mechanics more clearly.

8: Edit File Matrix Action Revamp
Edit File is not an opposed roll if you are the owner of the file or have permission to edit it. Similar to the Control Device Skill, editing some kinds of files require you to make a different skill check, such as a profession or performance, with Data Processing as the limit. The File defends with the matrix attributes of the Host or Device it is on.
Setting Protection on a file includes setting a passcode to allow access to the file, similar to how Data Bomb works. Using the Passcode can allow access to the file for any of the normal functions of the Edit File action, but also for removing protection if desired.

Reasoning: Edit file, as an opposed roll for even a spell check, and it's lack of a legitimate way to access a protected file, did not sit well with me. Similarly the defense attributes of a file being based on it's owner but not the device it's on unless it's a Host was a bit strange to me. Now it's non-protected defense have everything to do with where it is.

9: Control Device Matrix Action Tweak
If you are the owner of the device, or have permission to access it, you do not need to make an illegal Sleaze action to control the device.

Reasoning: Control Device is written as if it is only used by a hacker, and thus requires an illegal sleaze action to do things like "eject clip" on a smartgun for which you have 3 marks. This doesn't work so well for the security guard mentioned on page 237: "A security guard's weapon might be in her holster, but its owner is the corp that employs her. " This setup makes it similar to Jump into Rigged Device, which doesn't have an opposed roll for users with permission.

10: Defining Permission as Invitations
A mark gained through an invitation is considered a legal mark. If all your marks on an icon are legal marks, you are considered to have permission for any legal actions for which you have enough marks. Owners always have permission to use their devices.

Reasoning: A few matrix actions define different rules for users with permission, but MARKs in 5th edition have replaced the permission scheme of past systems. The rules seem to be intended to keep hackers having to make skill checks to make use of their hacked MARKs on a device, but the way it written it gets in the way of legitimate use of a device, so "permission" is mentioned but not defined. Instead of adding "permission" back into the system parallel to MARKs, I want the two be the same thing.

11: Cracking File Protection
The Crack Protection matrix action can now be down as the user's choice of Attack or Sleaze.

Reasoning: Limiting Crack Protection to Attack means that a successful cracking of protection, which is necessary to view or copy the file, automatically alerts the owner or Host. That limitation removes the idea of a silent matrix run from being possible in many situations. By allowing a Sleaze action, it becomes possible to crack a file without setting off an alert, although failure to break the protection would cause an alert and get you Marked by the file's owner.