Solenoid D controlling clutch 8 would be the common one for the gears you’re missing, unfortunately, reman ECMs can be like this on occasion. It’s worse when it happens after fighting and fixing another problem concerning the same ECM.
Maybe this might help. Here are both Test Point Diagrams and the list of clutches. IIRC Clutch #8 solenoid is the inside one on the bottom, closest to the transmission.Is the bottom outs side solenoid the right solenoid for the gears missing? Dealing with these solenoids is kinda a pain. Some say solenoid d or 4 but it run clutch 8 I think and the wiring diagrams are weird too.