I lost the reverse gear in my 91 Accord AT. I replaced the trans with one from a 93 Accord and now have an unusual problem. When the car is started and driven it runs fine until you accelerate usually after about 2-3 mins. At that point the rpms flutter a bit and the car acts like it's "missing." You can also hear a relay kicking on and off under the dash(fuel relay maybe?). If you accelerate the car will go, but the problem returns immediately as soon as you start cruising again. The cruise control works even with the car "missing" so I ruled out the VSS. I jumped the solenoids and all four have good hard clicks, not weak. No engine check lights, no flashing S indicator, no D4 flashes. Definitely feels like an electrical or computer problem. I am stumped. Any ideas?
additional info:swapped out the TCM and reset memory on the ECU and still no codes and the car functions correctly for a test run but then it returns to the same problem. Except now when I accelerate it continues to act like it's "missing".

 

These aren't fun

There is a tiny, yet very important ground on the t-stat housing. Please check it to be sure it is clean and tight.