Originally Posted by viola-tor
Brakes seem fine, chain seems fine... But keep the ideas coming! It'd be great if it was something silly/easy.
I just read through this thread and it seems like you've been chasing this issue for a while. Why not just put the bike back to stock (emissions crap back on) and test the mileage to see what you get? Seems easy enough to do, and will immediately rule out a number of possibilities. It will cost you next to nothing assuming you kept all the parts.