There should be no functional difference between the 64 bit and 32 bit versions of the game, except that the 64 bit game will not run on a 32 bit computer, but those don't really get used anymore. I didn't notice that you were installing duplicates of the mod until you mentioned there being a 3rd mod. The GitHub main and 1.9 should be mostly the same though the GitHub version may have fixed one or two things. Either way, installing two versions of the mod is a sure way to cause problems.