So. I kept the Ohm meter on the positive and negative battery cables (battery disconnected), and found that with the key on, it showed ~1-5 ohms depending on how long I left it on. I pulled each fuze individually, and when I pulled the 15A fuze, the Ohmmeter showed an open.

I put the fuze back in and started unplugging connectors, when I unplugged the CDI (Part number on the module is 2737220311) the ohm meter showed an open.

Is this making sense? Do I have a bad CDI? or is there anything down from the CDI that I should be checking?

 

You haven't really done anything to diagnose the problem other than replace a fuse and check the key switch, but you were close to the problem.

Here's what you need to do: unplug the wiring harness from the key switch - looking at the pic below, you will see when the switch is ON, terminal A is connected to terminal F - this is the ground connection - you need continuity from A to F. At the same time C is connected to D - this gets power from the battery to the red/blk wire.

Now go to the fuse block (here you have to start paying attention to the wire numbers) - wires # 151 & 152 are carrying power from the key switch to the fuse block - 151 goes through the 15 amp fuse to wire 153 and wire 152 goes through a 10 amp fuse to wire #170.

Since you were blowing the 15 amp fuse concentrate on that circuit:
Wire #153 goes to the LH handlebar switch - inside the switch when in the run position, terminal D is connected to terminal E of socket 1 and terminal D or socket 2 - terminal E of socket 1 has no connection, but terminal D of socket 2 connects the red/blk wire to the red/wht wire #158

The red/wht wire #158 goes to a splice where it junctions with red/wht wires 157, 194, 156, 160 and 159

157 goes to to the brake light switch - no problem here unless the fuse blows when the brake is used
194 goes to to the CDI box - potential problem
156 goes to to the gear position switch - turns on the neutral and reverse lights - no problem here at the moment
160 goes to the last 10 amp fuse in the fuse block - there it becomes the org/wht accessory wire #164 - it has nothing connected to it unless an accessory has been added

Now the key switch is not ruled out as a problem because it has to make the system ground connection - look back at the pic of the key switch - wire 174 is the chassis ground - it is junction-ed with 181, 183, 041, 172, 017, 038, 068 and 195 - a poor connection of the lug to the frame could cause a fuse to blow - now back to the key switch - 174 is connected to 173 (note 173 is not connected to the frame lug)

Wire 173 goes to to a splice where is branches into 193, 056, 148 and 181 - a poor connection at this splice could cause a fuse to blow

Wire 193 goes to the indicator light panel - if the lights work, the ground is OK
Wire 056 goes to the throttle safety switch - not normally a problem causing blown fuses
Wire 148 goes to terminal B of plug 2 on the LH handlebar switch - it connects to the engine kill wire when the switch is in the STOP position - not known for causing a blown fuse
wire #181 goes to the ground lug assuring ground even if the key switch is faulty

To get power to the lights and such, jump from the + side of the battery to a red/wht wire - if things come to life the problem is either a faulty key switch, faulty LH handlebar switch, a faulty connection at the plugs on the LH switch or a broken wire.

I have the wiring diagram in PDF if you need it - here it is and you might be able to copy and enlarge it

 

Thank you! That wiring diagram is a lifesaver! I did pull out the title and ran the VIN number, turns out this is a 2010, not a 2013. But looking at the wiring diagram, I don't think there is much of a difference.

I had a few minutes tonight so I disconnected the CDI box, because when I do that the short seen at the battery terminals goes away.

I unplugged the LH switch and key switch, they rang out correctly for all positions.

I checked Wire 173 and 174 at the key switch to Negative Battery, both are a short (.3 ohms)

I plugged the battery back in and turned the key switch to "ON": Headlights and brakelights work, dash lights work (except my Neutral light is burned out but I verified I have power on the connector when in neutral). The Engine OFF switch turns off all the lights. I didn't try to start it since the CDI box wasn't connected.

I took a quick look at the CDI box, There is a short between the BK/RD (Switched Power), WH (Stator position sensor), and the BN (Ground). I think I may have found the short. At least I decided to order one of the cheap CDI boxes off Amazon (if this works, I will probably sink some money into a better CDI).

I also ordered some thinner probes, so I can do a better job tracing the wiring harness, and to measure othe stator and ignition coil.

 

New CDI will be here Wednesday

 

Wiring diagrams while drawn differently are nearly identical

 

Follow-up: I finally got some time to put it all back together. Using the wiring diagrams, I was able to verify the coils and check out the rest of the harnesses.

Put in the new CDI box she started right up. I had to use the pull cord because the battery is shot after being shorted for so long, I charged it for a couple days and it would drop to near zero volts when I tried to use the electric starter.


thanks again for your help and the wiring diagrams!