Progress Thread Cracked The Thermostat Housing 2000gt Conv

My 2000GT convertible after 15 years of great service just cracked the thermostat housing. I am considering replacing the intake with the Ford racing intake. Since I am going to have to replace the intake, I was thinking what other mods I can do to increase horse power.

Currently I have a K&N Cold Air Intake and I replace the cat-back with a MagnaFlow Exhaust. What do you guys think?

I replace the busted intake with A FORD racing intake. I ran into some problems with the install. First problem: The intake manifold to head gasket is different on my car. It appears that the heads on my car are different from the other GT's out their. I was able to get the right ones after going to the local FORD dealership they were able to look up the correct gasket with the VIN number. The dealer told me that FORD had figure out that their was another head that would work on these cars and they used them on that model year.

Second problem: The thermostat gasket housing didn't fit correctly on the new manifold. The old one had a spacer that fit as guide for the thermostat housing bolt. The new one didn't come with it so their was a 1/4" gap between the bolt and the housing. To correct this I had to make my own gasket to make the housing seal.

Third problem: Car starts up fine and idles ok until you run the car for about 1/4 mile, then it starts to run rough. Can't figure out why it doing this.

Any help figuring out the misfiring would be appreciated.