Another O/D Off Flashing Thread :/

[Big99]

Vehicle
Early 1999 Ford F350, Super Duty, PSD, 4x4
210k Miles
Major service was done at 178k

Mods
Napa Big Filter Kit
Additional Fuel Filter
Hypertech Stage 3 Tune
EBPV Gut
Straight Pipe

...And the story goes,

Two days ago, I repainted my dash, took the whole center dash off and unhooked all connections. My OD light never did work, and I never had OD problems. However I did notice a wire burned through its coating and appeared to be shorted out. Anyway, replacement of the shifter with the OD harness solved the light not working. Now, upon starting of the truck, about 30 seconds into it being started, the OFF light starts to flash on the OD switch. My transmission shift fine and smooth. Only thing I notice is that it doesn't shift into OD. Before I used to drive @ 65mph @ 1700rpms, and 70mph at ~1900-2k rpms. And now, I am at 65mph @ 2k-2200rpms. Another example would be me driving at 41-42mph and it would shift into overdrive and drop my rpms to ~1100-1300rpms. Now im at 1600-1700 at 41-42mph. So obviously I've got NO OD.

Question is, why is it that after I took off my center dash, and fixed the OD light, that caused the OD not to work?

I've had VDSS replaced also, I was getting intermittent speedo. Anyway, I'm going to hook up my Hypertech and see if it can pick anything up.

Meanwhile, any suggestions? Thanks.

Hypertech DTC Results

1249 - Wastegate sol. (Mines off, did the pedestal gut) - Cleared.
1690 - Wastegate circuit failure. (Ok, makes complete sense still) - Cleared.
0500 - VSS Failure (Ok, right on, I replaced this yesterday, ABS light has been off since and speedo working) - Cleared.
0743 - Torque Converter Clutch Circuit Electrical (Okay, this one sounds major and expensive, what am I looking at here guys?)
0381 - GPR (Well, this has to be an OLD code, because everything related to the GPR including the dash light, are functioning as it should) - Ideas?
0475 - (Hence of the EBPV gut.) - Cleared.
0478 - Exhaust Pressure Control Valve High Input - ?
0470 - Exhuast Pressure Control Sensor Circuit Malfunction - ?
1211 - Injector input code (Due to a programmer, normal) - Cleared.
1139 - Water in Fuel Indicator Circuit Malfunction - Nonsense code, cleared.

All codes were cleared, another check came up with the update below.

***UPDATE***
After clearing all DTCs, 3 popped back up, and caused the OD Light to flash, once again.

The DTC Are as follows:
1249 - Wastegate solenoid (This is due to my EBPV, this and the 1690 will always be present, however they do not override the OD function)
1690 - WGC
0500 - This is the VSS code, Not sure why this came back again, I replaced the sensor. (However, I know that this relates directly to the OD function, so I think I got a break)
After closely looking at the VSS on the rear differential, all wires seem to be OK, however; in one spot, where there is a ground from the bed to the frame, the ground wire is pinching the harness that leads back to the VSS, and rear electrical. I will be disconnecting that ground, free the harness and open it to inspect for any wire tears. If this is not the cure, what should I look for?

Concluded that the P0500 is the culprit of my OD issue. Rear VSS is fine. Replacing the sensor on top of tranny, upon inspection, I saw that the clips for the sensor were broken, leads me to believe when the shop replaced my main seal, they broke the clips, possibly damaging the sensor. What does lead me to believe that its the sensor is the fact that even after clearing the DTCs, the P0500 comes back instantly after start up. Meaning unresponsive sensor?

Hopefully my grief and troubles will help someone whose searching.