Make the car the way you want it. Right now, unless the car is a 100 point car it is only worth what the right guy is willing to pay. Doing the swap will not require you to do anything you can't un-do to make the car "original" again. Just store all of the take out parts away and have some fun.
My car is a 3 owner unrestored real numbers matching car. But due to the combination it is not really that desirable to a collector. I bought the car in close to original trim. The way it sits now is far more driveable and WAY!!! more fun. And that is what it is all about.
Anyone can restore one, it takes a real man to cut one up!!!