Here are some houserules I have been working on. Please critique and let me know if I am missing something.

Since my view of the matrix is crucial to understanding where these houserules came from, here is a quick note on how I see the matrix.

1. The entire matrix is a mesh network. Please see a short wiki article here and another short article here.
   
2. The fact that the matrix is a mesh network is why you can snoop, hack, edit, etc. on the various live data stream swirling around the various wireless nodes. Old-school tech, such as shortwave radio, walkie-talkies, etc., are immune to edit programs (and their cousins); however, they can be jammed at the drop of a pacifier by a toddler with his Sesame Street™ Commlink (Rating 1) provided he is close to the source.
   
3. Joe Average™ uses a program rating of 1, maybe 2. Corporate wageslaves use rating 2, 3, and 4 programs depending on their job description. Rating 5 and 6 programs are rare beasts indeed.
   
4. The costs for the various matrix items bugged me. Yeah, personal bias - sue me.

General Houserules

1. All matrix related items (hacking programs, agents, commlinks, etc) are Availability = Rating x 3
2. Costs for all programs are doubled
3. All Common use programs are automatically available at System rating - 2.
4. Commlinks must be purchased at Cost = R^3 * 100 + R * (S - 1) * 100

Example on comm costs: Response 4 / Signal 4 (max availability for character generation) -> 4^3 * 100 + 4 * (4 - 1) * 100 = 6400 + 1200 = 7600.

Specific Houserule
I wanted to separate this one out because I am still tinkering with it. In order to lessen the BP load on the TM. I am planning on two things:

1. 1 BP = 3 CFP
2. Skinlink

Complex Form Points:
Each BP purchases 3 CFP to be used to purchase CF per otherwise normal rules.

That a TM can manipulate the EM field in the open air with her mind and can't manipulate the EM field around her own body just bugged me.

Ok, there they are. Please critique.

Regarding your assumptions:
1) True.
2) True. You can't edit live wireless broadcasts, not only "old school" transmissions as you said but also from "new tech" wireless transmissions like commlinks. You can't jam transmissions with a commlink, you need a jammer to jam transmissions (hence the name).
3) Makes sense.
4) Huh? Why?

As to your houserules:
1-4) Why?

Ok, point taken on the jammer.

The houserules on cost are a reflection of my bais that they should cost more.

House Rules:
1) Okay.
2) Sure, why not?
3) No big deal.
4) Umm...I...it...I guess if you enjoy formulas, go for it.

However, these are all just relatively minor tweaks on matrix stuff. Usually when I see matrix house rules around here it's for stuff like capping program hits and making logic matter and trying to stop Agent Smith - you know, stuff trying to make the matrix work. These house rules of yours are fine and all, I don't think anyone's going to be up in arms about a commlink coming preloaded with an Edit program, but they, well, they're really not that exciting for hackers in your game. If you tell the hacker your house rules are to make some availability and price changes on programs, they'll shrug and go, "Meh."

TM Rules:
1) I fully endorse this. You might also want to adjust karma costs for improving CFs.
2) No arguments here.

I'm actually less convinced of the Matrix being a mesh network than I am that it is a bus network, or more precisely a series of overlapping bus networks.

Prolly because everyone else's stuff costs more. So why should a hacker get off easy?

Just my two cents and perspective.

It's because there's no such a thing as a pure hacker anymore. Bunker babies are so 80's. The hacker role has been absorbed into the other character roles. You have to be a tech savvy cyberninja now. Since no matrix test use Logic anymore, you can play a retard cybersam blockhead as an uberhacker with no problem. Technomancers are all that's left of the hacker class, and they don't seem to be very playable.

@ Buster
Ok, now I understand. (Must be the hours I'm keeping recently...)

No, I don't want the bunker hacker back at all. I just want there to be a separation between the sammie who hacks little old ladies comms for extra beer money (kinda like the script kiddies who phish for Mom's Account on Amazon) and the dedicated hacker who stands a chance against a Rating 6, IC ladden, security spider monitored, corporate system.

My hope - please note that the commlink rules aren't play-tested yet - is to persuade fewer PCs to choose to try to be the sub-hacker.

NOTE: For me, this is a departure. I hated the Matrix rules in 2nd and 3rd, so even allowing a PC hacker is different for me.