Keep all the original parts, and don't change anything that can't be changed right back. Anything that is missing, or changed will be a $$ deduction, when it comes time for you to sell.
If you change the trans, or put the original engine on a stand, the next owner will deduct to put those back in. Not everyone has the same taste, you usually won't get back what $$$ you spend on modifications.
Maybe to you it doesn't matter. It's only money right?
If you have a very rare car, IMO it is better to leave it authentic, and build a clone to enjoy.