My V6 GT (ignition problem)

I installed a new carb, shortly after (i don't think it has anything to do with the carb, i had a guy who builds race engines install it for me) the car started running really poorly, we took the temperatures of the header primarys and the #2 and #3 cylinders were running really cold compared to the other cylinders. there isn't any noises coming from the engine, so i'm pretty sure that the engine components aren't broken. but we also tested the spark strength and it has a really poor spark off the coil. The coil is a year and a half old flamethrower 45,000 volt coil, the roter and cap were installed in september, and I have ford racing wires, recently tested them at 1000 ohms/foot. Could the ignition module have gone bad or what else could it be,(plugs are new also, but probally fouled from not firing). If it is the ignition module, i would like to go MSD, which module from them works with our cars, also i would prefer if it had a 6k rev limiter.
Thanks, and any feedback is appreciated.
-aj

it is a 302, but like i said above it has 2 cylinders that are dead, therefore only 6 are working, thus V6

the spark coming from the coil to the distributer is the spark that is really weak, i don'tknow if the bad cylinders are getting spark at all.

well... now it seems to start out with the dead cylinder, at least it feels like it did when the cylinder was dead, then i rev it up a couple of times and the car works just fine, pulls hard and smooth, has a smooth idile. but the start up still signifies that something is wrong. what could it be?
-aj