Won't Crank until cool? :(

[HoodStrype]

Hey guys I've had this problem since October and I'm at my wit's end...

After driving my stang for about 20 or 30 minutes, once it's turned off, it will crank but not turn over again. After a few hours, it will crank. Twice it wouldn't crank and after 5 min it cranked again. WTF??? Usually, after about 20-30 minutes of driving it will start to hesitate somewhat. It's died on me a couple of times as well. I'll try to list everything I've tried:

I've changed the
*distributor
*dizzy cap
*rotar
*battery
*alternator
*tps
*Idle air bypass
*plugs
*control module
*coil twice
*starter solonoid
*unhooked and rehooked up msd 6al (still died or wouldn't start with or without it)
*checked timing 3 times (13*)
*checked for spark after coil (I think it was mostly successful)
*Fuel Pump always primes
*installed Fuel Pressure Guage on rail... getting 39psi at idle
*fixed all vacuum lines (still a high pitched noise coming from lower intake)

I have no idea what to do next. I've spent all of my money on this thing and I can't even drive it. Plus my clutch just went out last week so I can't drive it again to fix the problem... ugh.

Also, I think it was coincidence, but it didn't start this problem until I put a 1" spacer between the u/l intake.

I'm so lost now, any help would have me driving my car for the first time since I bought it last July- thanks