I always start with a 2x2 stone foundation for the 'center' of any of my builds, and build around that, because that cross + section in the center of them will always be centered to the rest of the build, and offers a central point for a support beam (if necessary). It will also act as a guide point for the uppermost levels of any build, and makes rooftops easier to seal.

Given you've already dumped a lot of time and effort into the build, breaking anything up top to gradually come down to find your error that rendered it off-center, or to fix inaccuracies in the design to fix the roof is out of the question now. The best thing for the roof now is to likely make a singular cross section up top (horizontal beams), and try to manage sealing it that way by finding the middle. Otherwise, tearing down the upper portions until you can locate the offset is going to be your own viable solution, unfortunately.