from all indications your stator is had,I have found that the factory tests for the R/R are inconclusive especially if you are not really sure if you performed them correctly.
If you feel the R/R is bad which it sounds like it probably is you may want to consider going to the newer and cooler running,MOSFET type R/R ,there are several members on here who have and most have had nothing but good things to say about the upgrade.
I definitely agree with denny that testing the R/R is not exactly the easiest the first time, but I find them to be conclusive during my testing. I guess your mileage may vary depending on your meter.
(Some?) aftermarket R/Rs test the diodes both ways, while the stock R/R has one way diodes (I am not an electrical engineer so if that is explained incorrectly.. sorry).
Personally, I did not go the MOSFET route, but not because I have anything bad to say about it. A pulled R/R off ebay was cheaper and I was broke
. I went for a stock R/R that was in good condition off a Ninja 600 (same part#), and I get the full 14.5v charge @ 2,300rpm. No charging is occurring at idle, which the MOSFET can do - big bonus there. Isn't the downside to the MOSFET the fact it does not have the 6th cable that turns it off when the bike is shut off? I think I read about current draw at all times, so a few installed some switches. Worth a search on the boards at least.
What I can say is do not buy some cheap-o new R/R. The one I replaced was less than 6 months old apparently, seems to be the cheaper $60 one sold on eBay from overseas.
I would possibly research a little bit on the diode testing and see if you can get some verifiable results. My third stator connector on the cheap-o r/r tested bad (solid tone), and two of the three tested bad on the old stock r/r that was oddly still mounted on the bike (one solid tone, one infinite reading). The used one I ordered on eBay passed all the tests first time around, and is working great.
I guess the real question is, could a bad junction box end up frying the r/r, which in turn, killing the stator? *CSI Glasses*