i know my shifter is way off cause i have to lift my foot OFF of the peg to shift up.and i think thats what screwed up my tranny so had the tranny rebuilt and now looking for a fix to the shifter problem.
i dont have the mids on anymore i have fowards but i think their not the right ones for my bike

 

I have stock fl controls and I have to lift my foot to shift, its because of the relativly long throw of the belcranks

 

Probably nature of the beast on ratchet lids ! If you don't already have one you could try a toe/heel style shift lever (FLH style ) I never did like this style one some of my FX's but got use to it on my 93 FLHS ( no ratchet lid system )

 

Lifting your foot off the peg should not have anything to do with a tranny failure unless you were jamming hard it in to the next gear.