Stator help with baja dual sport kit

Just bought a 2000 XR650R and it has the baja designs dual sport kit on it and there was a short in it so NOTHING worked. After we had a few guys looking at it testing every wire until we figured out the previous owner (assumedly) had a gps or something else hard wired in, then unwired it, saw the wires were both black (probably a home-brew to splice in 12v outlet) and then connected the two wires (hot and ground) and shorted the whole thing out. When we got that figured out, the battery took a little charge (charged it for not even 5 minutes) and then the lights, blinkers and everything worked perfectly, until the battery died. The stator isn't charging the battery or powering the rest of the stuff. Shouldn't the baja kit run directly off the stator once the bike is running? We were wondering if I could have fried the branch of the stator that the lights and accessories run off of, does that seem likely? Anyone know how to test that?

Could have easily burnt out the stator, check each set of winding for continuity, you will probably find 1 set has gone open circuit, also check non of the coil circuits go straight to ground...indicating a burnt winding.

Here you go check the alternator part of the image, you can see the 4 wires coming out of the top of the alternator (stator) each pair is 1 coil.....

The regulator (AC or DC) may be fried, thech it - and don't wire it out of the circuit, you'll need one.
Yeah, a stator can fry, by that's easy to see & measure normally.

I tested out the continuity of the stator (black/red and brown) and that has continuity, as do the green and white/yellow wires, so I assume that means the stator is okay. The green and white/yellow wires go to the rectifier as in that diagram, but I have two solid white wires coming from them instead of the green and white/yellow. So where it t's off, one of them is green (from stator), green (from rectifier) and then a white one (I haven't traced to see if it goes to the headlight/tail light yet since I had to go to work), and the other one is a white/yellow (from stator), white/yellow (from rectifier) and then a solid white (also haven't traced this yet). Unplugging the stator wires and putting my multimeter in those connections showed continuity, but when I unplugged the white wires and checked between those two I had no continuity. So the green s (stator), green r (rectifier) and white 1 are spliced together and the white/yellow s, white/yellow r and white 2 are spliced together, I get continuity between green r + white 1 + one end of multimeter where green s was plugged in and white/yellow r + white 2 + other end of multimeter where white/yellow s was plugged in, but not between green s + r + multimeter where white 1 was and white/yellow s + r + multimeter where white 2 was. I know my explanation must be near impossible to follow but I don't have my bike near me to go take pictures unfortunately. I'll try to draw up what I mean on paper and take a picture of that and upload that in a minute.

Make sure they don't go down to ground with continuity, this would cause a short

okay, here is what I was trying to explain. I'm working until 9pm tonight so I won't be able to check and try to follow those white wires until tomorrow probably. But shouldn't they both have continuity?

Only 1 pair goes to the rectifier and the other pair goes to the ignition module ? as per drawing above ?.

I haven't traced the white wires to where they go yet. I'm starting to think I fried my rectifier though, I'm reading several threads on several forums and it seems most people are talking about bigger rectifiers than the 650r has stock, so I'm assuming that there's a reason they use bigger ones, but I don't know. I'll have to have my neighbor help me with it, he's way better at these things than I am. I have no clue what I'm doing.

Edit:
Just want to add something: The bike has a 12v outlet (AWESOME). I want to hardwire in my GPS to the DC side of things so that even if the bike is off the GPS stays lit up and on. I want to run the 12v outlet off of the AC side for charging phone/camera or whatever else, potentially heated grips in the future. Anyone see any issues with that? Also, how do I know which coil is running AC and which is DC? The stator only puts out AC and then the rectifier converts it over to DC correct?

Won't matter which coil is used, but white and green are the stock ones. The stator puts out power all the time the engine is running if your not using that power it has to go somewhere....into the reulator which dumps the power in heat form, if you go for a higher power regulator then you would need a higher power regulator to disipate the heat it could produce, where are you going to put the battery ?.

it has the battery behind the front light under the cross bar, was thinking of putting it under the seat though. The guy who installed the bd kit left the stock wiring harness in there as well so I think I'll remove that today and clean it up so there are less wires, because right now there is no way the battery would fit under the seat. I also gave this forum misinformation, I guess that's the problem with typing it out while I'm at work without the bike in front of me, trying to remember it all. The white wires come from the stator. The stator puts out like 8 wires, which wires are for the coils? None of the diagrams I've found online have the correct colors. I have a green and brown wire that wasn't plugged into anything, so I plugged in a light to see and started the bike up and it was indeed giving the light power and turning it on. So I was thinking of running the power from that through a rectifier and then into the battery instead. So when the bike is running it still runs from the battery right? The power goes from the stator, through a rectifier, through the battery and into the lights right? I'm wondering if this guy ever had the ds kit working in the first place.

ok, so I managed to get it working! YES! Thanks everyone for all of the help. I have it running off of the two white wires from the stator. I don't have the 12v accessory plug working yet because I want to run that off of the other stator coil so that 1) I'm not drawing too much from the one and nothing from the other and 2) so that it'll turn off when the bike isn't running. But I'm not sure which wires to tap into for the other stator coil. Out of the stator I have 6 wires: 2 white (one coil that is already being used by my lights/ds kit/gps when I tap that in), a green/white and blue/yellow wire that are in a plastic connection piece thing, a brown and black/red wire (which I think is my other coil, and I can't unplug them because if I do the bike won't start), and another green wire and white or gray wire that go no where right now. Would I splice the 12v cig lighter thing into the brown and black/red wires?