Holy cow man...
I recently had a flex plate break and while pulling the trans the tc was stuck to the flex plate. So I had to reseat the tc on the trans. I was sweating the entire time thinking about your issue. Lol..
It's going to be up to cust if we run it unplugged or dive deeper.
Like said it's an 05/06 with egr doodled but he claims it was never tuned but no cel and no 1408 egr codes... It's got to be tuned.
I even pulled over, plugged back in and didn't make it 150 ft and knew the issue was there, turbo over boosted and low power. Unplugged, then rung every gear out 26/28 psi awesome power, can even lug it in 3rd and it'll spool right up.
300k miles, original injectors.
Denso starter
5w40
Stancor relay and motorcraft glow plugs.
No issues starting when in negatives for days, not plugged in..