Craig S.,
The answer to your question is very simple.
Imagine TWO IDENTICAL cars.......one with it's original engine, the other with a replacement. It doesn't matter whether they are '68 Baldwin-Motion Phase III Camaros, Hemi Cuda convertibles, or '49 Nashs. One one with it's original engine will always be worth more.
Of course, there will be cases where due to different equipment or documentation between 2 cars, the one with the replacement engine may be worth more.....but to answer your original question, I think we (you) need to consider IDENTICAL cars in every aspect other than the engine....
