HELP! MAJOR PROMBLEMS! expert advise needed.

I have a 1990 FORD MUSTANG LX 5.0 SUPERCHARGED1990 lx 25th anniversary car...original paint, original interior, original motor with 65,000 miles with this list of mods..

tremec 3550 tranny
aftermarket clutch
ford aluminum dirve shaft
welded in subframe connectors
3:73 gears
5 lug conversion with moser 28 spline rear alxes
Vortech V-1 T - Trim polished supercharger
msd ignition
ba 2400 mass air meter
42lb injectors
sct chip tuned by the designer of SCT( jerry *** have dyno sheet..on mustang dyno ..395 hp 398 tq
GT-40 Aluminum heads
ford racing shorty headers with x pipe no cats (have stock h- pipe car passes emission in CT no problem)
Flowmaster american thunder mufflers
anderson power pipe
cobra intake.
E 303 cam
two core radiator
tokico shocks
H&R sport springs
Maximum Motor sports chrome caster camber plates
Maximum Motor sports heavy duty lower control arms with heavy duty ford uppers
Maximum Motor sports lower a-arms with low friction ball joints.
Maximum Motor sports urenthane streering rack bushing
Auto meter phamtom II boost oil pressure and water temp. guages.
1995 polished cobra R's ( bought used when did 5 lug conv..wheels are not mint)

Now for the problem...
I recently was trying to trace an oil leak...I replaced lower intake manifold gaskets. At the same time I replaced the stock fan with a stock replacement, a new stock ford waterpump, and a new serpentine belt tensioner. Right after this install the car started to run hot, must have over heated and now I have blown head gaskets. This car never..NEVER ran hot before unless is was 100 degrees and you were trying to get it hot. (donuts, burnouts..fun stuff) I had a litts test done and it came back positive and a pressure test and it builds pressure in the cooling system fast. It is not blowing white smoke out the tailpipes. Once it overheats it boils over into the overflow and spills out.
Could I have installed the lower intake gaskets backwards?? I am at a huge loss to this car and everytime I take one step forward I get two steps back.
HELP!    

You're going to have to check the stupid little stuff on this one. First of all, what intake gaskets did you use? The water passage of the intake gasket, did you trim off the excess so the water could flow? The water pump, are you sure it is a reverse rotation unit? Is the belt routed correctly? Have you tried a new thermostat? Are you still using the factory fan clutch? How old is that? The symptom you speak of is a result of the blown head gasket. Have you already changed out the head gaskets?  
Michael Johnson
Associate Editor
5.0 Mustang and Super Fords