I gave the injectors a cleaning, they were spraying perfectly and the bike when it was running was very, very strong....I even did that "mach chicken" run with the baton one day and it was a real monster....Since you said that the fuel filter was dirty, I would think that the injectors would need cleaned as well, you may also have one failing.
Cleaning them is cheap and easy.
Or, there are a few companies on ebay that will sell you reconditioned(cleaned with new filter caps and o-rings) oem Bosch injectors for under $100.
Filter cap and o-ring kits are around $20, if you only need those.
The stock filter caps will clean, and the o-rings can be reused if they have not torn or hardened(put vaseoline on new ones).
Maybe not your issue, but something to consider.
I've noted that even when getting a little heavy handed with the throttle lately it will pick the front tire up in a shift from 2-3rd which is something it didn't do before that I noticed...
Like I said, this is a real head scratcher...