Ok, so I recently acquired a '99 VFR from a local guy. He was a member of the VFRDiscussions board and has a post over there about his work on the charging system on his (now mine) VFR. I know the 3 Honda bikes I have most experience with... VFR, VTR, XX... all seem to have similar rectifier and charging issues.
Just thought I would bring this up to you guys... click the link for his "fix"....
Beef up the wires!
He only ran the bike like this for about a month before I got a hold of it, so it isn't known if this is a true long term fix. It does take care of the voltage fluctuations though.