This isn't going to be easy, building a frame without the correct tools is going to be a chore, if you don't gett it straight its never going to be strong, it will end up handling like shit and you will end up have problems with it.
A custom driveshaft can be made pretty easy. I would suggest having one made for you. Again, if these aren't straight I've heard it could cause the car to flip or just end up not working correctly. This could also enable you to use whatever rear end you could make fit.
As for the rear Suspension. I couldn't tell you what to use but an upgraded S2k sounds decent.
I'm not to familiar with the s2k trans but I know the shifter position will defenitly not be the same as the stock civic one. You are going to end up cutting holes.
Exhaust should be pretty simple, although the driveshaft is going to take most of the middle section, but since you said this is going to be practiucally built from the ground up that should be easy to route to the back of the car.
You will have problems with wiring, but I can't say much for that, I suppose the engine and car could be converted to obd1 for convinience and performance. It shouldn't be that much of a hassle but it's going to be time consuming. i couldn't tell you what ECU to use but a Standalone system is probably going to be a very good investment.
When you have some more questions I'll answer them as best as I can.