Original is always best!
Yes, hold on to the original motor even if you decide to put in something else. That motor is worth a lot when it comes to originality and that specific (or one around the same build date) car.
I'm about half way through de-cloning what the previous owner had done. De-cloning a car is also expensive! If I didn't love the car, I'd sell it and go out and spend even more on a more original car.
One rule of thumb is to keep all original parts. Someone else might want what you do not, and someday when you decide to sell it will make a difference. And if for no other reason, we owe it to the hobby...