2006 Exp XLT 4x4 5R55S Transmission has 2nd but intermittent O/D.

[Witsend06]

Hello I've got a 2006 Exp XLT 4X4 5R55S transmission that can't figure out. I recently repaired it, and installed a shift kit, everything looked fine. The cause of the malfunction was a broken snap ring becoming lodged between some friction plates and the flow control valve was bad. The case shows the servos bores had a bit of wear as expected, but barely noticeable(maybe .005-.007 t.i.r). After installing the transmission I filled with fluid to the appropriate on an even surface. And topped it of at close to 100°F. I reset the shift tables by disconnecting and isolating the negative battery terminal and connecting a section of wire with alligator clips to the positive terminal. Waited ten minutes and then allowed the idle values to correct. And shifted thru each gear and waited for about 10sec. before shifting to the next gear.
When I went on the test drive the transmission shifted great. It only had maybe 1-2 shift flares. I thought it was completely fixed. Everything seemed to function perfectly. I could engage both H/L 4 wheel drive, no noises, the O/D on/off worked fine. No codes no wrench light, it drove and shifted perfectly. I thought It was fixed.
The next day I wanted to test it on the highway. No problem at all initially, then around 65mph the yellow wrench lit up. No CEL just the wrench, the tach was at 1800-1900rpm. No bad sounds or noticeable decrease in performance. I pull over, stopped, and turned it off. Restarted it and the wrench was gone. So I took off and like before gradually increased the speed up to about 75mph. No problem, no wrench, drove and shifted fine.
The problem is reoccurring now. And to me its seems to be 5th gear(O/D). I've got 2nd, and every gear. But the wrench can come on anywhere between 40mph and 75mph. It seems like O/D is malfunctioning but how it might, is beyond me. Since I've still got 2nd and everything seems to be working great. After the wrench light comes on, the O/D on/off no longer works. But the rpms don't increase at all. It's been about 10 days now and it still hasn't thrown a single OBD code.
Sorry about the length of this, i wanted to be thorough. Any ideas or suggestions to look would be greatly appreciated.

 

[Witsend06]

Update:
Still hasn't thrown a code. I've taken it to two auto parts stores because my obd2 code reader is fairly generic. They couldn't retrieve any codes either. It still runs and drives decent. I noticed some frayed wiring on the maf sensor and taped them up. I'm getting about 16.5mpg after fixing the harness. If i can figure out what's up with overdrive I can easily get even better mpg. Some other things, cruise control works the entire time, even after the wrench is illuminated. And when the wrench lights up. The O/D on/off no longer illuminates. But i can watch the tachometer and see that the rpms are being effect when i toggle the bhtton on the shifter. Is that even normal?

 

[Witsend06]

3 months later and the exact same things are still happening. Still runs and drives fine, and still get the same powertrain wrench light without any codes.

 

[JK080]

Not all scanners can retrieve transmission codes especially with a Ford, you may want to find a shop that can scan it for you and see what they get. Based on your description of when the problem occurs it would seem to me you may be having torque converter issues.

 

[Witsend06]

Not all scanners can retrieve transmission codes especially with a Ford, you may want to find a shop that can scan it for you and see what they get. Based on your description of when the problem occurs it would seem to me you may be having torque converter issues.

JK080,
Thank you for those and any other ideas for me to check. I thought that might be a possibility. The torque converter is about a year old and I believe it's functioning properly. It's not slipping, there's no shudder or noise, it takes off and shifts up/down thru every gear like it should. The transmission isn't leaking a drop. I've had 2 national auto parts chain stores hook up their in-house scanners. And my neighbor is a owner/operator of his own auto mechanic shop. He used a professional grade updateable Snap-On reader and a real nice Actron scanner that was updateeable before grabbing it. None of the 4 readers had any codes stored at all. Just the illuminated powertrain wrench. That goes off and stays off after turning the motor off. Until the next time it comes on again that is.
Because it (powertrain malfunction illuminates) repeatedly shows a problem. I believe there's a problem.
I've been curious if I might need have the TCM or PCM reprogrammed possibly, since I installed a shift kit? Any possibility of that being the potential remedy?
Thanks again, I appreciate any and all input on the matter.