So, looking over the text for the Simsense Booster and the Encephalon, I find myself with 2 major questions and various smaller ones.

First - Does a Simsense Booster provide a TM with an extra IP when he goes hot-sim naturally?

Secondly - Would the Encephalon provide him with bonuses to electronics and cracking, since they work fundamentally different from a normal person's use of those skills. (Tertiary - rating 1 provides a +1 to all logic active skills, that includes cracking and electronics? And the rating 2 simply provides just those 2 groups with an additional +1?)

and finally... not a cyber question, but, Intuitive hacking, for either a hacker or TM this means they use Skill + Attribute instead of Skill + Software/CF for the selected action?

Even for a TM, these are still Logic-based Active Skills.
Encephalons don't give a damn wether they provide a bonus to mundane software programming, TM threading, spell design or improvised neurosurgery they just do their job which is applying "a +1 dice pool bonus to all Active Skill Tests using skills linked to Logic".

The level 2 would most likely also include TM versions of said skills for the +2 bonus.

It augments your information-processing abilities, wether you process said information via Resonance or not shouldn't bother the device.

The question of the Booster still bugs me though, it doesn't state that it only works through commlinks or exclude TM usage. Also, I realize that TMs are still processing simsense signals, they simply do it directly, without an implant. Obviously the effect would not stack with Overclocking.

The Encephalon determination makes perfect sense, of course, I was merely wondering if there were any other thoughts on the matter, similiar to Cerebral Boosters providing drain dice for certain traditions (or platelet factories/Blood Circuit control preventing some of the physical drain).

You'll always find someone who claims "it's technology, it doesn't work with magic" if you look long enough, but these claims are unsubstantiated 99% of the time.

There may be basis for the discussion that cyberware shouldn't work with magic/resonance, based on personal interpretations of the fluff, and one is free to feel that way, but the rules are clear that they do work normally by RAW.

there's a comment in augmentation by netcat that she knows a TM who used one of the hacker-improving pieces of 'ware (i think it was 'ware... may have been nanites) that messed him up. but she didn't know if it was him, or that he was a TM...

so, basically, it's left up to the GM. the implication is that maybe it has negative side effects.

Tis was nanoware, personally I think I'd rule that the doctor in question simply "glitched".

I always just read that as meaning that even getting a teeny bit of 'ware messes up a TM's natural abilities (i.e., Resonance) to a significant degree, which it does. I don't think there's an intent to imply even worse side effects, or it'd probably appear somewhere in the rules as well.

I don't know, I don't think Resonance Loss would manifest itself in the manner that Netcat decribes.