Nope, one computer for the engine and transmission.
If the OD OFF light is flashing, then there is a transmission problem and likely a P1728 code which means slippage. In an effort to "save" the transmission, full line pressure is commanded and you get the harsh shifting you describe.
Time to figure out what the code is and go from there with data.
The problem with the 95-97 PSD trucks is that the PCM cannot differentiate between a torque converter clutch slip or a direct or overdrive clutch slip. The 99-up trucks have an input shaft speed sensor so they CAN.
You can throw parts at it all day long and still not fix it. I recommend actual diagnostics.
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Tuning, flashing, burning chips, and repairing all aspects of 7.3L Powerstrokes.
SEVEN 7.3L-powered vehicles in the driveway. Two didn't come that way from the factory!
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