if i use the gmst cleaner on all my mods will it affect them adversely or cause instabilities in my game or would it be alright? the reason i am asking is because i downloaded a number of mods and they said they would be need to be cleaned of dirty references so i am basically wondering if it would be alright to just clean them all because i can't remember all the ones that need cleaning.

It's safe to delete the "dirty" GMSTs. Some plugins change the GMSTs intentionally, make sure you don't delete them.

EDIT:

I forgot about the dirty references. tes3cmd and testool can clean them out