Okay let's assume I removed, dismantled and repaired (since there is nothing wrong with it) and now I have reinstalled it...how do I move the swash plate to align the hole in it with the stop bolt?
I have dismantled and reassembled one Kubota HST of different model, but in general the pistons inside the HST motor cylinder block are spring loaded in order to get the initial seal in-between rotating cylinder bloc and valve plate.
This spring-loading is pushing the thrust plate away and preventing you from aligning the thrust plate hole for the stop bolt.
When it's disassembled there is no spring loading and you can reinstall the stop bolt.
There is plenty wrong with your HST now:
You may need to custom make a new proper stop bolt to fit your buggered re-threaded hole in the aluminum housing, or better yet get a replacement housing.
New stop bolt in manually re-threaded hole may not be perfectly straight and cause problems sooner or later ?
I would start looking for a used replacment HST if the rest of the tractor is in good condition and would not recommend installing a new bolt made in bench grinder in case you plan on keeping the tractor!