Yeah. A is a big pain, and I think why half of everyone's waiting for the rigger book to come out. For now, I'd think that you could try putting internal tookits and such into a drone as though it had cyberlimbs.
B is handled by the tables on page 231, but I'll give you the skinny on how you deal with. First, if you're not going to start off with a lot of drones besides your body (and perhaps a backup), don't split your RCC's device rating between Sharing and Noise Reduction, just put it all in noise reduction. Also you'll want these programs for your RCC, roughly in this order: Signal Scrub, Encryption, and Biofeedback Filter.
Also, invest in Electronic Warefare, as you can roll it and get the hits as extra noise reduction. Now, any noise left after all that is applied as penalties to your actions taken. For emergency body defense, buy a few meters of wire to replace the default one meter one you're getting and plug it into your body. As long as you have a wired connection, jamming, noise, and all that won't matter to your rigged in actions.
It can matter for your wireless bonuses, but that's why you'd want a high rating commlink to slave non-drone weapons to.
For a practical example, assuming that you have the second worst rig and have Signal Scrub running, then you'd take no penalty for being 1 km away, your drone behind 5 meters of metal reinforced walls, if both of you were in a rating 2 spam or static zone. If you were instead 5 km away and you were in an abandoned underground place, then your rolls are all losing 3 dice, but you're probably pretty safe. So if you have good initiative, take one pass to roll Electronic Warfare + Logic and each hit gets rid of one more die of penalty.
Same goes for if somebody starts jamming you.
EDIT: The above was written before you posted your expenses. Although I don't think you need the hotsim in your commlink. The RCC has it by default. Unless you wanted it in there for other reasons. Then you might want trodes, if you aren't going to spring for a datajack (which also gives more noise reduction). And you might then want to note if the autosofts are on your RCC or the drones. It matters for the sharing if you're going to use it. Which you might. Signal Scrub + Datajack is still an okay resting Noise Reduction and it lets you run all the softs off your RCC but the Electronic Warfare one.
And since I'll be by my books for a bit, if anyone else wants my two bits on a question, ask away. I'm going to be looking for answers to other questions, like does PT cover geneware. (I'm sure it covers other metatypes because they're all still humans, so to speak. See Earthdawn and questions about interbreeding, etc. etc.)
EDIT: And I did a little while editing in for the stuff said above, and here's my soft rule for Prototype Transhuman and geneware. Anything that's in Transgenics or beyond is definitely beyond the limits of PT. Now to look over the rest of the thread.