yeah, i read up a little bit on the cam, but from the sounds of it, you have more than enough mods to support the engine and it's power level...
the eec-4 is a very versatile and complicated piece, it's going to make adjustments to fuel and spark based on a myriad of information...especially coolant temp-when it's in warmup mode, it runs a little richer to bring up the temp, when it reaches op temp, it leans them out for normal operation. when it gets hot it pulls timing and fuel to try and cool the engine down a little
and with a 4k stall, well, from what the rec. on the cams page at AFM, thats a little high, but i'm betting it used to get up off the line in a hurry...
the heating issue...man, honestly, i would've stayed with a stock style pump, and gotten a thicker rad. the cooling fan may not be pulling enough air to keep things cool though, and when it gets hot, it's gonna run weak for the same reason as stated above, since 5.0's don't have a knock sensor, the computer has to compensate for "safe" levels of timing lead and fuel enrichment based on how all the sensors are reading and referenced off of preprogrammed operation "maps"...i'd try to tackle the cooling problem first though...the only thing that might remedy it at the moment would be to try putting on your engine driven fan and see if that helps or hinders your situation, if it helps then you can bet the fan isnt' pulling enough air, if it doesn't you've got other issues...
we're working with a friends '95 Cobra, and it's got some problems getting warm too, a 331 with normal bolt ons, and a better rad have yet to keep this damn thing cool...but we think the cooling fan just isn't cutting on soon enough.
i gotta get going for a bit though, duty calls, and it's probably gonna be awhile-but there are several highly knowledgeable people on here that are well versed in the operation of the eec, and they could more than likely steer you in the right direction...hope this helps a little bit at least