Stay stock and use bolt ons if possible
It's a mystic cobra, but I don't think it will be worth a damn except in maybe 30 years.
All SVT's are rare; the Mystic, Cobra R, Pace Cars, and Mystichrome models being the rarest. As far as higher values in the future, you will need the car as close to stock as possible when you goto sell it. This is where bolt ons versus motor swaps help. Can you imagine someone advertising their "rare Mystichrome Cobra" for top dollar after painting it Grabber Orange?
The sc is about 4k? The rebuild and labor are what I can't guess at. Another 4k in parts and labor?.
The down side to the 4V is the limited selection of internals. The FR500 heads are going to run you around 1500, the new FR500 valve train and cams another 1500, plus about a grand for forged pistons, rods and a crank. You still need new seals, lube, etc. You can shop around and find the best deals, but this still doesn't include labor. Nowadays, shop rates are high. I can't see getting a rebuild AND new FR500 parts for near $4K. You
might be able to get your stock parts reworked for that price.
One guy said to me "I'd wind of having to charge so much you could build a nice 5.0 with what I'd have to charge you for the headwork and cams alone".
Yup. I could have gotten a killer 347 Stroker for what I paid for my Mach 1 crate motor, but all the money I saved would have gone to modify everything else to make it work. I spoke with Ford Racing before I ordered my crate motor to ensure that the 03 would "drop right in and go". They said yes. None of the coil on plug connectors matched, the AC lines where all different, I had to reuse my old power steering pump, and the ECU plug needed some changes as well. So the $6K for the motor (which was "discounted" by the way) plus the labor to remove, rewire and reinstall the motor may have gotten my Teksid rebuilt with FR500 goodies and it would have BOLTED RIGHT BACK IN! Hindsight is 20/20. At least I still have a DOHC (with 12 month warranty) under the hood even though it is not the much lusted after hand built SVT flavor.
On a side note, have you already completed or planned out the other upgrades you'll need? 500 HP is not going to sit well with stock fuel pumps, air meters, injectors and brakes. Is your transmission going to take the upgraded abuse? You will also need to beef up your chassis. Someone here said it best....
"Speed costs money, how fast do you want to go?"