I have a 2006 F550 with a service body I purchased last year. Truck had a Fummins conversion performed by PO. It has a 2003 24V 5.9 installed with kit from DCS. It has custom transmission tuning to accommodate the swap via SCT and has light engine tuning but not turned up too high. My normal operating weight is around 18,000 lbs. PO installed a custom heavy duty torque converter built by Larry Barnett. He is big in the Fummins swap community from what I gather. Truck has approx 10K miles on it since the swap was done.
Back in May, I was driving the truck and it felt like I hit a bump in the road. It is heavy and rides like a wagon, so I didn't think anything of it until the Tow/Haul light started flashing. I used the SCT and pulled codes and it had P0741 and P1744. I cleared the codes and drove the truck again, and after it hit 4th gear and the converter tried to lock up, the light started flashing again. I've been through several threads on here and other sites and the consensus seems to be either the TCC solenoid, wiring, failed clutch in converter, or stuck TCC valve in pump.
I have checked continuity and resistance on the wires from the PCM to the trans connector and they were in spec. I went ahead and dropped the oil and pan to change the solenoid. Oil was still nice and clean. There was light metal debris on the pan magnet that I would consider normal wear. Not excessive, just fine particles. I checked the internal harness and found no issues. Solenoid ohmed out in spec, but I changed it in case it failed mechanically. Replaced filter and filled with new oil. From what I read, the Valvoline max life synthetic was the oil to use. Test drove truck with same results. Trans temp was running around 160 deg F with maybe 10 miles of stop and go driving. I can confirm that the TCC doesn't engage. The SCT doesn't have the ability to monitor lock up (or I'm not smart enough to find it). We started planting operations so I didn't have time to pursue it further at that time.
I've finally gotten back to working on it. I pulled the transmission this morning and removed the torque converter and pump. I drained the converter through a rag and there was no debris present in oil. I checked the valves that are visible in the pump without disassembly, and they were all free. I am at a loss on it right now. Short of loading the parts cannon or putting it back together and taking it to a shop, what other checks can I make?
I've been a mechanic for 24 years but I work on heavy equipment. I usually despise working on automotive, but I can't afford to take it somewhere right now.
I'm just looking for advice. Most of the other threads I've seen just trail off after a short while with no real fix or diagnostic info.
All help will be very much appreciated.

Edited to add that since I've had the truck, I get an intermittent stutter when I shift in to reverse and start backing up. It usually on lasts for a few seconds when it does it. Not sure if it's related or not. Transmission seems to perform normally outside of these issues.