I would guess Ford Racing was telling you the truth. The ECU doesn't have any drivetrain parts to control in a car with a manual transmision that is cruising in 6th gear. What the ECU tune "could do" is shut down the fuel injectors faster, when you take your foot off the throttle, to generate more aggressive "engine driven deceleration." The "thump" you are feeling certainly is likely from "slippage" in the clutch, transmission, driveshaft or differential, but it could be a loose motor mount or something else that is reacting to "hard engine decel." I would consider going to another dealer - one that sells Ford Racing Performance Products in the Baltimore area - and get their "drivetrain guy" to drive the car and observe the problem. Even if you take off the tune, there is almost surely a "physical issue" in the drivetrain.
What I don't understand is, shouldn't I have some sign of bad part while on factory tune? weather it be a bad motor mount, lose u joint, lose LCA, play in the differential, etc.. etc...???? I'm a little lost because I have no sign of anything being wrong when I'm on factory tune. Then all of a sudden, as soon as the procal goes on now I'm getting excessive clunk only in 6th gear when getting on throttle. Now from doing my own little research it does look like these cars have some slack from factory, and which is probably the reason why so many peoples talk about clunk when they shift or clunk when cold clunk when pushing in the clutch and etc..etc.. I'm sure the 2 pc drive shaft is much of the reason for those clunks in question, and for those reasons, most peoples learn to just live with it because its just the characteristic of mt82 drivetrain. I don't know what is exactly changed within procal calibration but I do agree with you that procal does not change anything within the drivetrain setting on manual cars. However, I'm almost certain that it does change the TPS calibration for better throttle response which somewhere within the tune is causing my "drive train slack" to come alive. I was actually talking to [email protected]
and he also agree that the transition within procal calibration for TPS seem too abrupt as long as I am correct about having no issues when stock, which I have NONE fortunately. So, If I take my car into the dealer with procal tune I'm sure something will be fixed because its that excessive, but if I take my car in with factory tune I am sure there will be nothing to fix because there is nothing to be replicated because there's just absolutely zero clunk within the condition I mentioned. I know you are saying there must be something wrong somewhere if I'm having this clunk issue after procal, but to be honest, I don't think I do. I believe this is simply a simple tuning issue that I happen to suffer from using a "tune for all" deal. After all, this is a mail order tune that is not custom calibrated for each and every car. Maybe that's the reason why some get pinging and some don't, and I get more excessive clunk than say xarious who seem to have the same thing going on. Other MT82 guys with procal have zero issues. Maybe all this could be simply fixed with a simple datalog and remote tuning but I guess it is what it is.