Well that is unusual to say the least. I wonder, when you insert it and find it to be at an angle, are you passing it through the shifter fork, or do you have the fork out? Just speculating the fork may be bent and forcing the pin askew (???)
EDIT: Pondering on it a bit more, I’ll bet the guy that worked on it before you came along ran a tap into the hole crooked (cross-threaded it).
