You will need the pedal box off a valver and fab it into the car.
Late 8v had the brackets ready to go, what year is it?
You don't need hydro unless you are going for power, which would be an engine and box change anyway.
I'd save the money until then.
Patches on the sills is only a temp fix imo, also budget for some floor/inner sill work to join the new outer sill section.
Sun roof can be a real pita, check the drains first a search on here will throw up loads of information.
Rust is your main enemy, it's been sitting and you know about the sills.
I'm betting you have a few bungs rotted out and others, so check thoroughly before you take on Mk3

Every thing else is easy and cheap.