904 2-3 shift flare

I'm about to start on the rehab of my Duster and 1 of the many things that I have to deal with is rebuilding the wide ratio 904. This trans was built about 12 years ago by a friend/tech at a local Dodge dealership. After installation it had several problems that I can't recall any more, that led to me removing it and disassembling it a few times. Eventually all of the issues were fixed, except 1, RPM flares during the 2-3 shift, when the shift is made with the lever in D. This only occurs at full throttle. In normal driving or when shifted manually, it shifts okay.
My question is, when I tear into it, what should I be looking for, specifically?
I'm probably going to switch to a manual valve body, but I want to make sure that the problem is fixed, not just band-aided.
I will be doing the work on the trans myself.