Yeah I messed up. After I bought my bike, I changed the oil in the F4i with a Moly brand (I was new to street bikes and didn't think there was a difference). As soon as I figured out that I'm not supposed to use moly, I changed it. I put about 2000 miles on the bike with moly in. I've noticed the bike shifts much smoother.

Any long term damage? Could I expect shorter clutch life (or a more serious problem) in the future?

 

You'll be fine.

I always notice better shifting after an oil change.