Pilot bearing

Ok so i got my parts(correct spring, plastic washers, and new clips) from brewers in and it tightened up my linkage. However, i found my problem elsewhere. First, the downrod was snagging on the boot but the issue is with the t/o bearing. Specifically the spring clips that hold it on the fork. The lower clip is stretched/bent. That's rather disappointing because means trans needs to come back out right? PS, those clips are a PITA. *Actually the more I think about it I'm not sure that could be it because the fork goes all the way back anyway. It must have to do with the linkage still.*