The 1994-96 12-valve CTD is a fantastic engine which will last forever with proper care. I loved my '94. I sold it to my brother and he's still driving it.
The biggest problem is the torque converter lockup, which is weak. That's what ultimately went in my 1994 CTD with 47RH, at somewhere around 400,000km (248,000mi). Hopefully when yours was overhauled they installed a more heavy duty torque converter with 2 or 3 clutch packs.
The 1994-95 had the 47RH transmission. 1996 was the first year for the 47RE. Not sure if there were other problems specific to the 47RE, but I don't believe there were many differences. They didn't switch from a kickdown cable connected to the valvebody to the stepper motor under ECU control until later years when the engine went throttle-by-wire. I think that started in 2003 with the HPCR engines.
From my 1994 CTD experience, if the trans starts going in and out of lockup at steady speed on the highway, the problem is the TPS, not the transmission. Also, the TPS has brass eyelets in the TPS body where it bolts to the bracket on the engine. If you knock those out, it makes the mounting holes bigger. Then you can rotate the TPS to fine-tune the speed where it shifts into 4th gear and when the lockup happens, to suit your driving style.
Adjust the bands and do fluid and filter changes with ATF+4 as per the service schedule. Do not skip on adjusting the bands. When towing, start out in 1st gear, let your foot off the throttle, upshift manually to the next gear, then get back on the throttle. Don't just push the tow/haul button and let the trans shift automatically.
If your truck shudders/lugs after the lockup engages until it picks up RPM, you probably need to replace the overflow valve on your injection pump. This shuddering can also cause driveline problems such as lockup slipping and eventual failure if not corrected.
LarryB's 1 417 413 047 Overflow Valve for Dodge Cummins w/Bosch P7100 94-98.5 - Dodge Fuel System Parts - Dodge Cummins Diesel LarryB's