So you had one of these pass-through sensors, with the signal going straight to the PCM?
https://www.dakotadigital.com/index.cfm/page/ptype=product/product_id=57/mode=prod/prd57.htm
Then you converted to NP241 40-tooth tone ring and had the tune adjusted from 8000PPM to 40 PPR. The PCM also needs to know the ratio between your driveshaft speed and vehicle speed, which is essentially the differential ratio and tire size.
Assuming speed sensors are the issue, datalog the transmission input speed, engine RPM and vehicle speed. I think you can also log current gear if that helps. If the signal integrity is bad, you would see the VSS dropping out or erratic. If the math is bad, you'll get the wrong ratio between those speeds. It does shifting based on VSS, not RPM, so an error can make it shift too early or you can only reach a shift point as very low throttle position. Does your speedometer work? On your drive, hold some known speed steady for a while so you reference that to a known speed at the same time (like GPS).
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You've wired the 2 wires from the VR sensor directly to pins 20 and 21 on the PCM or is one of them grounded?