Car dies, I'm out of ideas.

[Three02much]

I have a 95 gt, with a 347 and aluminum heads. When i got the car running with the new motor i noticed that every once in a while on the highway the car would randomly miss, just once on one cylinder. but it wasn't like a miss, the best way i could describe it would be a hiccup. when it happened it felt like the motor quit for a split second and jumped back to life, more violent than a miss would be. I figured it was because i haven't had the car tuned with a chip. So This problem maybe happened once a month. so the other day the car completely shut off, except for the gauges, so it had power. Then i tried to start it, it would crank for three seconds, fire and die. Then after letting it sit for a while i was able to start it and get the motor revved up a little, once it fell below 2000r's it died and didn't start like before. I replaced the pickup coil, and checked the coil, now the car starts but wont rev up over 2500 r's Next im looking at the ignition module. it has good plugs and wires, good fuel pressure. what else could it be, maf? oh and the air conditioner doesn't work anymore, blowers work but no cold air.
any ideas would be greatly appreciated.