Just tossin out a ? here,
As others have posted when doing the kind of rework of the cab you have mentioned that they X-Braced the door openins and across the cab to keep em square so when they cut out big sections like the floor,roof,back window an such that the cab didnt twist all up, ya may be dealin with a problem like that if you did not?
Seems your cab went CATTIWOMPUS on ya durin the replacement of all the sheetmetal ya did and now is in a twist.
As far as a FIX ...I have no advise...I'm sure someone has been in your shoes an will offer up a way to go.
GOOD LUCK
Tim