Ha, I'm actually struggling with this as well. I picked up a beautiful Scarlett Red 88 GT that has 43k original miles, speed density system and immaculate condition. I've already got a huge stash of parts sitting aside to include Edelbrock heads and intake, long tubes, mass air conversion with 44lb injectors and PRO-M 75mm MAF. I'm taking delivery of a new 347 stroker motor on Sunday for it as well with a Comp cam in it.
While I want to keep the stock parts, I want to build an entire powerplant and drivetrain separately and then pull the factory system out and preserve it. I will even put a tubular k-member in the car. What I will NOT do is weld in subframe connectors or do any gauge pods or anything that will require any sort of drilling of factory components, firewalls or fenders. It's a tough thing to do and I've been here before, cars usually end up completely modded but since the value of these cars is going up over the years I do think it's important to preserve them the best you can.
That's a nice car and you should try to keep it as stock as possible, or at least maintain the factory components, ensuring you have stowed them properly.