Here is my take on this subject of originality and numbers matching stuff.
i have seen too many times where someone swaps out an engine from a low production car like a cobra. Of course you are not going to swap a low mile well kept example but just because it has a lot of miles you still kill the value. An example:
Saw this the other day, not sure if these will post up as I copied links off IG. 93 cobra with a 5.2 aluminator stuffed into it. Pretty sick build, that went to SEMA. Thing sounds like a beast. View: https://www.instagram.com/p/B3idNUsgxBp/?igshid=40mwg6blohyg
www.stangnet.com
His attitude was it already had well over 100k so it was ok. And it is a really cool build but being a 93 cobra he used the wrong car. I feel that car was in too nice a condition to modify like that. He could have used a gt. Just because you can does not mean you should.
Keep the engine and if you have it the trans too. Stick another engine in it if it suits you, it's your car. I think in terms of value in specialty cars because I've seen too many cars that would have been worth more money with the original drive train even if it was clapped out junk. JMO.