so it's the motorside... damn for the life of me I can't find a pic of the 04 R1 with out it's fairings showing the left side.
we have a few R1 owners... they may be able to help you figure out if something is wrong... I know I've seen several things when work'n on motors that look like they're bent or tweaked only to find they're made that way...
the only reason I say this is cause unless it's just a complete coincidence... I don't think the water pressure would cause that...