For towing and all of that, I'd use the 6.0 engine. We have a video in the multimedia section that is of a 4x4, i believe he is running a 6.0 in his ext cab 4x4 and smoking ppl and the motor has tons of tq. The 6-speed will bolt up (i'm 99% sure of that)..
The mileage really isn't a concern, seeing as 60-100k motors are still running strong, but if you are going to abuse the piss out of it, you might look for lower milaged motor.
The 5.3 trucks are nice, if you like the looks, get a v6/5-speed and swap to 6.0/6-speed, but if you are doing it to save a little in wiring/mounts than an older chevy, the price difference will more than makeup for the price of those small parts.
Now I would do this option, altho I like the 99 and ups, but here they are still a pretty penny (about 13-15K for a ran down 5.3 RCSWB). I like the older chevy's personally (well, 95-98).
By compatable do you mean will a truck PCM run a camaro? If so, yes.. but will have different tables, etc. on it. But yes. all the ls1 and ls1 variants all share wiring.
The stock gauges will work as far back as 94, later than that, not sure. Allens (fartruc) used all ls1 sending units and his 94 gauges work. The temp gauge is 1 line off, but nothing big.
Yes, the 6-speed will bolt up. 
The ls6 IM will only help you if you are looking for speed. The 6.0 intake manifold has longer runners, making it produce more low end torque. Altho, Allen said in a post under ls1 conversions i believe, that the ls6 and 6.0 manifold doesn't show THAT much difference up top. Just the 6.0 has more bottom end.
I'll throw this in.. the 6.0 exhuast manifolds only flow slightly less than shortie headers for the trucks.. so if you do that route.. save some cash and get those instead of spending 400-500 for shortie headers.
91 s10 - bagged and bodydropped...getting rebuilt
91 nissan - backhalfed and bagged