Not so much crazy.. I just don't think you know what you are getting yourself into. You need to have much more from the S2k than just the engine and rear axle.. Electronics, driveshaft, etc.. Who knows how the prelude frame will even handle that.. You could be doing quite a bit of welding.
I say plan everything out before you even consider buying everything. Find a wrecked S2k, see how much that is.. Good luck finding one under 5K. Same with the lude. I'm sure this car will be very nice the way you have it in your head, but there's many many obstacles to overcome first.