I'm not convinced that "not sitting level" is a result of the torque tube cracking. To my knowledge no one else has reported this particular problem as a manifestation of the cracking issue. On the other hand, there are numerous reports of loaders that don't sit level on other tractors (check out posts on the Kubota
B3030 from a year or so ago, other tractor brands involved too) where there has not been any cracking issue. I think I recall that lack of level has been reported on brand new tractors too.
Your FEL use sounds minimal and certainly not severe duty. I used my cracked KL120 quite aggressively with a grapple and despite putting heavy and sometimes asymmetrical loads on it I never saw unusual flexing or distorted level of the bucket. Most of my 180 tractor hours were grapple use and I often lifted the rear of the tractor while digging out stumps etc. The cracks did extend over the course of a year but not nearly as badly as yours did. I wonder why 1) your cracking is so severe and 2) how that could lead to not just more flexing but a fixed 1.75 inch distortion.
As a general point, tractor FELs are not nearly as strong as bulldozer blades and using them do do more than simply lift dirt/sand etc could potentially twist the arms so they are slightly out of alignment. Either lifting an asymmetric load or hitting an obstacle off center when "bulldozing" could potentially damage the long arms of a tractor FEL. These things are not reported often so I'm not saying that the FELs are weak just that by design they are more vulnerable than we'd like to believe.
Has your dealer looked at the loader? Is the bucket itself straight?