HELP! 95 GT cuts out while driving?!?

I have a 95 Sunfire GT that I bought needing an engine. Put in a lower mileage engine and the car runs great...except that it cuts off from time to time, and all the warning lights come on for about 5 seconds. When the car cuts out, it is only for a second. Can anyone put me on the right track? Also, is it normal for the temp guage to fluctuate? I have owned only imports until this car and the temp never moves on all my previous cars. On this Sunfire, the temp stays halfway while highway driving, but goes to 3/4 in traffic, but not quite to the overheating mark...Thanks in advance.

located the computer under the passenger headlight, removed it, and pulled all wiring connectors. Then I cleaned the computer, and put it back on, making sure to completely plug everything back in, and so far, no problems. I think that solved it. (knock on wood) I have put 12 miles on it without any problem, where-as before, it would cut off several times in a mile. I hope this helps someone else with the same problem.
I still wonder if the temp fluctuating is normal...

I've read stuff about the 95's getting hotter in traffic, but as long as it's not causin problems it's prolly not that big a deal