Both the CMP (Camshaft Sensor) and CKP (Crankshaft Sensor) have a critical clearance or air gap that is set by a thin piece of cardboard glued to the sensor, the idea is to "bottom out" the sensor when installing, and then the cardboard spacer comes off and the gap is set. Make sure they installed both sensors properly, because there is an adjustment bolt holding the sensor in place and it needs to be properly positioned and torqued upon installation.
You are doing good to keep a '96 running this long. You didn't give the mileage, and the 3.3 is a sweet engine, but have you been faithfully doing all the other 100,000 mile interval items. I can see you've done a couple of them. The sensors are a hit and miss failure item, no way to tell when they are going to fail, but did you maybe get a another bad sensor, it's been known to happen.
Provided they flashed the new PCM properly, i.e. up to date software, I doubt it's in any way related to your transmission. There is communication between The PCM and the Transmission Controller, but there is no way the CMP/CKP signals would affect the transmission.
If you are doing fluid and filter replacement at reasonable intervals that 41TE should last a long time.
Question: Where is your trans fluid going if it needed to be topped up?