Well, to get back to Acheron's original question.
I do not believe doing your motor up would affect the resale of your car negatively. (as long as you kept EVERY nut, bolt and part you replaced to reach your motor goals.) ability to put it back to original Saleen stock.
I would have to say that if I was in the market for a used Saleen 99-04, and had the choice of purchasing a nicely done E-motor upgrade in an original (Saleen) car )like what Acheron is proposing or a nice low mileage E car, I would have to go with the E car original.
This is simply because there are two types of Saleen buyers.
1. The guy who wants an original Saleen and is on a limited budget.( in which case he would not be in the market for Acheron's car because I am assuming that Acheron would want to get the extra value in monies out of it he put into it. ??? (motor upgrade) That would put his car out of reach of that consumer.
2. The other Saleen buyer like myself (an old guy compared to most of the guys here) would spend whatever it took to land a clean, used S281E to meet my wants/needs. The guy that will plunk down 48-55 grand on a 02-03 S281E is a very small niche customer. I know because I am one.
Like I said earlier, Acheron would want to get some of those dollars back I assume?
If you want that kind of rwhp do what some of the others proposed and build your motor anyway you want. Just don't build it in anticipation of selling your 01 SC for an E-Car price. (no offense implied) It is a fantastic concept, but the pool of prospective buyers at that level will go with an original E car.
Look, you own an original 01 S281 S/C. It will always be that. Build your bottom end and purchase the Series V blower. Pick up a max-grip diff and S351 center exhaust while you are at it. ( those center pipes rob a few horsepower by the way, but I think they look fantastic! That's another subject. ) ( save your series 2 blower in a box ) If you ever decide to sell, configure it back to stock with the stock parts. SO what if you have built the bottom end. Just consider it into the depreciation. If anyone ask's, "yes, it's a Saleen" There are only a few hundred guys on the face of the planet that will be able to tell the difference between the two blowers anyway. I promise you will never get a guy asking you up front, " Is that an E -Car? " Most of the time it's "Is that a real Saleen?"
00s281sc386 has the best setup on his car for the money and performance. He can achieve E-car performance with a lot less money with that KB blower. That kit is fantastic!
Personally I would buy that guys 03 S281 S/C Cobra on e-bay for 42 large. Now that's the best bang-for-your-buck-in-a-authentic-Saleen-package I have ever seen. A new Cobra motor, and a numbered car. Do the usual 03-04 Cobra motor upgrades like intake, pully, chip and exhaust, and bingo. You have big rwhp #'s.
Building your motor to E car specs is more than just the bottom end and a blower.