O.K. I'm sure I'm going to miss some things but I'll try.
Starting from the front and working back...
You might need a thinner radiator so the fan won't hit.
The engine mounts should be carfully considered because that will determine how much modifying you have to do.
My '86 used stock mounts from the 350 and welded to the frame, my friends had a solid mounted plate on the front of the motor.
The two main concerns about space under the hood is the pass. side valve cover and the distributor. The heater box on the firewall might hit the valve cover so it might need to be notched out a bit. Mainly, make sure the distributor doesn't hit the firewall.
You need special headers, two of the primarys wrap around the steering column. I had to do some very intricate body modification ( BFH and an air hammer) to the underside of the cab to get the exhaust to clear.
Transmount may need to be totally custom, I used 1" sq. tube stock bolted to the plates that are welded to the frame.
I bought a Pro-Ratchet shifter and just ran the cable to the trans.
They make an ass load of kits to do this, Jegs or Summit, find a set of headers, radiator and fan, driveshaft depending on what trans your using and have fun.
And you might want to think about putting beefier springs in the front end, the weight of the 350 is a little too heavy for stock springs that are 15 years old. The stock ones will work but they might sag the front end.
As far as the nitrous, there's plenty of room in the bed to mount your bottle.