Kolt, Welcome and congrats on your purchase. So I am a little confused on the advice you are looking for. With a rusted body, you have to fix that first (unless it is in non critical areas and you want a patina car
). But you likely won't be able to save the original paint, since you have to fix the rust. Sounds like a pretty full resto (maybe frame on) is going to happen.
For the engine, keeping it all original but the intake and carb, will hurt value a little. You are not going to loose much HP by keeping the originals and making sure they (and everything else) are in top running condition.
My first advice is to not throw ANYTHING away that you take off car. A lot of things that you might not think, can be reconditioned instead of replaced. but the parts are also a good source of reference when comparing why a repro part does not fit. Once the car is completely restored, then you can sell the good parts and get rid of the rest.
So how about some pics and we can give you some info.