If you are concerned about future value, unfortunately yes, every change will lower the value. Anyone purchasing it will look at it as what will it cost to undo what you did.
This is really the same for any rare car.
So: 1) Not worry about the value and build what you want. 2) Sell it, purchase a clean body and build what you want. 3) Restore it, drive it, and then sell it if you want something different. Skip on the real expensive parts if finance is an issue such as carb and block. They can affect value, but not as much as personal modifications. Get the correct heads and repo manifolds. The color is actually really nice when done correctly.
