I need help, I'm a car guy with extensive experience repairing cars, but when it comes to motorcycles I need help. My problem is that my bike does not seem to be charging the battery at all. Shouldn't this motorcycle run fine even with a dead battery? What possible components can cause this? what do I check to narrow down my search?

 

its most likely the regulator/rectifier on the right side of the bike. Just below the large black box, is a smaller black box with 5 wires going to it. These overheat and poop out a lot. The best fix so far seems to be swapping it out for a GSXR r/r. There are some threads about that in the F3 forum, search around for GSXR in there.

 

No they won't run with a stuffed reg, (that is when it finally carps it), they will run sometimes because the reg death throes are usually intermittent. As Scrudog said, there is a GSXR transplant option, you will find that in F3 section. I replaced mine with a heavy duty replacement a few years ago with no further problems, although it did require a slight mod (another hole drilled into the backing plate). We are not alone though, the VFR's suffer from the same regulator job lot.
Oh, one final thing, if you do a check on the reg, make sure that the bike has been running for a while, you can get an ok readout if the reg is not hot (thats when they start to fail)
If you charge the battery & need to get it to the shop, remove the fuse for the headlight & you will get a few miles before the battery craps itself.

 

If you work on this on your own, look for damaged connections. When the R/R goes out from overheating, there is a tendency to melt the connections. It happens at the R/R connection and at the stator connection. Stator connection is under the tank and just forward of the battery. You will a bunch of plugs and it is the largest 3 prong plug.