I replaced the R/R but there is still no voltage increase on the battery while running. The R/R gets hot quickly when running so it must be getting juice. Fuses are good. Any Ideas?
jake

 

check the stator output
if it has approx 12.3v at 5k rpm and 10.8v at idle then that is probably it.

My VFR had the same condition. Replaced the R/R and still did not charge.
Replace the Stator (color was black , not brown) and had 14.8v.

 

I got about 10 VAC out of each of 3 stator conections but they are all the same. How can all three be producing the same and still be bad.

 

At 30,000 miles my battery was not holding a charge either. i replaced the flimsy honda regulator/rectifier with a beefier aftermarket one that had cooling fins on it ($80.00). Problem solved. Check the yellow wire that goes to the regulator/rectifier in your wiring harness under your seat-I bet it's getting burnt and turning brown or black!!! Maybe the wire is burnt through inside? Did you replace the reg/rec with a honda one? I'd definatly get an aftermarket one. the hondas have proven to be unreliable.