So heres a new problem for my 02 f4i. When I go to down shift it makes a grinding noise. It takes a bit to get it into a lower gear sometimes. But when I do downshift it makes the noise near the shift linkage only? Ive checked the manual but found nothing.

 

The rubber on your swinging arm may be worn and chain rubbing on it , Just a thought

 

I think robbie is onto something here. I would suggest maybe checking your chain free play. Is it very loose? I once had this same exact noise happen when I first started riding way back when on the first bike I had. When I would downshift and or sometimes just decelerate abruptly/chopping throttle, the chain would actually rub against the plastic chain guard and even the swing arm as well. 0.o My chain was shot and wouldn't stay tight. Check the swing arm and the plastic chain guard for chain rubbing.