Hopefully someone will be able to help me or point me in the right direction.
I have a 2002 Accord EX-V6. I've had problems with the transmission in regards
to the shifting of the gears. It is most problematic with the first, second and sometimes the third gear. At low rpm(1000 - 2000) the shifts are very rough, making the ride feel like a 15 year old learning how to drive a manual tranny for the first time. I've already had Honda look at the issue and they first replaced the solenoids which did not resolve the issue. They then replaced the transmission, but it is still giving me problems with the shifting. What I am interested in is what else controls the transmission? I am aware that there is a ECU but do not know how it will interact with the tranny or how to go about fixing it, if the ECU was the cause of the issue. My local honda dealer is not helping much, and it looks like another company just bought em out. Any help would be much appreciated.

 

Try a different dealership...

Was there any improvment immediately after they replaced the transmission?

The ECU is what controls the shifting of the transmission. If you suspect the ECU to be the problem, you can try picking up a used ECU from a junkyard, or swapping ECUs with someone else with a 01-02 V6 (I think the ECUs are different for 98-00 because of the different ignition systems).