Motorcycle Repair: yamaha electrical, alternator problem, fuse box

Question
I have a 1987 fzr750r that I have owned since new, it hadnt been run for about 5 years until october of last year when I brought it into a shop and had it serviced.  One thing they did was replace the brushes in the alternator but unfortunately the alternator needed to be replaced and as I couldnt afford the six hundred bucks for a new one, I picked up the only used one I could find for half the price.  After the winter was over it worked great and I have been riding it since.   A couple of days ago I came home and parked it in the garage and when I went out the next morning I turned the key and got nothing.  I figured the battery needed to be replaced so I did that and all I got working were the running lights, no headlights no neutral light.  I checked all the fuses with a test light and they all seemed to be ok but while I was doing that one of the relays near the fuse box clicked and I got my headlights and neutral light.  I ran it to temprature and shut it off.  I came out the next morning and tried to start it again and got nothing, not even the running lights.  I thought maybe the battery had gotten run down again and was shot so I put the charger on it for a while and pulled the ignitor box off and checked all that with the test light and it was ok.  I also was concerned that the alternator wasnt charging so I replaced the brushes in it and was able to push start it cuz there wasnt enuf juice to turn the engine over.  It ran for a while but the headlights were dim but would brighten whenever I gave it gas.  It suddenly shut down and I couldnt start it again.  Does this sound like an alternator problem, a battery problem or possibly that the relay is shot?  Im ready to take a hammer to this stupid thing.  Any suggestions Chris? thanks in advance.

Answer
Hi Jon.
 I see one of three possibilitiies here.  None of which are the battery or the stator.

1)  One or more of the fuses is bad, even though they test good.  The real test is to replace the fuses on suspect lines with brand new ones and see what happens.  Sometimes a fuse can test good on the meter, but not function within specs on the machine.  It is rare, but it does happen.

2)  One or more of the fuse connections is bad or dirty.  Clean the connections completely.  Worst case scenario means a fuse box replacement.

3)  You have an electrical short in the main power line somewhaere between the fusebox and the rest of the system.  This may require splicing one or more wires, or may require bypassing entire sections.  Worst case scenario would require a new wiring harness, which I do not believe is likely.

Check those and see what you find.
Good luck.
FALCON