One check might be to take a protractor and identify the angles on the T-Box output shaft and on the rear yoke. They ought to be close but the t angle should be a negative, lower than level, and the yoke should be positive, higher than level. The actual measurement ought to be around 3 degrees +/- a degree from being a level. if your t-mission angle is lower than 3 or so degrees then it I have to agree with 383 StealthRam on the possibility of a missing mount shim or... based on you having to remove the t-mission crossmember, did it happen to have spacers or shims between it's mounting flanges and the frame mounts for it that would have caused it to sit higher up, pushing the box up as a result?
Nick