Transmission woes
 

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?

I've move this to General Tech. Please do not post questions in the DIY Section