You will need to reflash the PROM. Easy enough with a computer, cable and TunerCat software. You will need to disable VATS, unless you transfer the whole ignition assembly (not worth it).
As for using your car as a donor....depends how much you can get for it as is, and how much you can get for a shell.
The PCM only controls engine and trans (if Auto). The radiator in the Z28 is too wide. There are cheap options though. Do a search on this site using LT1 as search word.
You will need:
JTR kit
radiator
hoses
fuel pump
headers (Z28 manifolds won't work)
Personally, I think it is not much more difficult than a carb setup. I had the carbed engine all setup in mine with a 200 4R until I found a great deal on a LT1/T56 combo.
There is tons and tons of info on this board. do a search and ALL of your questions will likely be answered.
Tim
BTW, before this, I had ZERO experience with fuel injection and with wiring up a PCM...it's not as hard as it may seem. Now I also have a 1994 Z28 for my daily driver (also a deal i couldn't pass up).