Jester, I would like to suggest you try something. Remove the inline gas filter you said you installed. Take the bike out for a run and see it this corrects the issue.
I experienced the same problem with a nice glass inline filter after removing the hidden filter( aka pain in the rear). Took it off, threw it in a box and no more issue.
I'm not running any filter other that the pingle in the gas tank valve. Been that way for 3 years.
