We tried both the Cummins crank sensor and a speed sensor from a 4L80E trans, neither would let the TCM do its job until the sensors signal to TCM was modified. Maybe both had the same wave pattern (dont remember) and we just needed to try the other type (at time did not know there were two). We went with the 4L80E sensor.
So, Will maybe you just need different sensor?
The TCM Eng Spd will function with a ISS/OSS for Engine RPM input to the right pin on the TCM. You may have to change the calibration to correct for the engine speed. (Yes you can make up a wheel or sloted wheel and place an ISS or an OSS close and it will serve as your ENgine Spd sensor. Two slots on the crak will work well. Or you can have 4 if you like. Only this spd will function for the Engine RPM on the TCM. (I hope this is clearer than the muddy water round here)
Back in 96 I took a Tech-1 and temporally powered up and connected sensors to a TCM with a prom installed.
I used a Engine Pick-up coil plugged into the wall socket (110v A/c) that was TAPED to another pick-up coil that was connected to a Ignition module from aprox 1990 4.3, 5.0, 5.7, 7.4L truck engine. (ead of the Pick-up coil plugged into 110v you can use a Weller trigger soldering gun held close to the sensor/Pick-up. It inducted the signal into these sensors ISS/OSS to test and see what Tech-1 would output. These ISS, OSS, and Engine Spd ALL read correctly with the pick-up coil plugged into the wall and the soldering gun. I did the math (pulses per rev for each sensor 31 for the ISS 40 for OSS and 4 for Eng Spd) and all read correctly. I was verifying other items as well but they worked.
I then tried the Ignition module with a pick-up coil taped to another that was plugged into the wall. I powered the module up to 12 v and grd. I used the Reference Pulse out and ref low or grd plane and fed it into the TCM for Engine Speed. It read double engine speed. (The TCM interrupts each drop or rise as a pulse.) I cut the calibration and it read correct RPM for the 110v 60hz signal I was inducing into the module pick-up coil.
(A trick I use to do for hard to start or Intermittent stall or stall no start was to get a Weller soldering gun close to the ignition pick-up coil (HEI or DIS) and test it. UNPLUG THE INJECTORS AND PLUG IN A NOID LITE. IT WILL FLOOD THE ENGINE and LOCK IT UP. I used Delco ST-125 Spark tester on the Secondary COIL WIRE. (On DIS I used a ST-125 on each plug wire)
THEN pull the trigger on the soldering gun and it will set the system off. I then would slowly move each connector or wire and watch/Listen for cut outs on the coil or injectors. TBI and Port Fuel work well for this test. IT was a trick I used when I worked on GM Buy-back vehicles in the late 80's. I didn't like walking in the MI 20 below winter. I did walk a few times before that.
Hope this will help all to improve things.