One thing I have learned from decades of experimenting is to spend the least amount of money possible while doing the initial fitup. If I can mock something up rather than purchase a costly part, I do that. The intercooler is an example. It isn't needed to get the engine in and running, but you do want to allow for the space required to add it later if desired. Even a completely stock Series 2 S/C will add at least 50% to the power available plus the manual trans will give a seat of the pants feel of added performance, although usually not actually true. A complete parts car with the desired drivetrain is a nice thing to have for all the small stuff and unplanned bits.
I just realized your car has already had the brake system replaced with a standard vacuum booster type. That may or may not be a help?
Every day something small, right? Today I ordered all the bushings for the front subframe, in accordance with the prophesies... Er I mean the helpful how-to's. Used the dorman part numbers from the writeup there, local parts house has them coming, will be here tomorrow. Just in time for them to sit while I work on the subframe.