Before I post my problem I would like to say I'm glad that BDK is now making the aftermarket KIPS valves in steel rather than aluminum. I believe I was one of the first members on here to post about the BDK racing valves back before they were making Steel valves.
Anyways enough of me trying to gloat about something I may or may not have done.
Here is my problem. I took my bike out for the first ride of the year last weekend. Shortly after leaving the truck there was a small point where I was giving it gas and the bike was trying to stall out. Before it stalled, while I was still moving, the bike picked up its momentum again and ran fine thereafter. Roughly an hour later we came to a stop and I stalled the bike trying to find neutral(oops). After this happened the bike did not want to start.
I pulled over to the side of the trail and checked spark, which I did have. I couldn't quite tell if it was blue or white or what color but spark was visible. I then removed the drain plug in the carb to check for gas, which I did. After this I kicked and kicked and kicked and nothing. Then my buddy gave it a go. Same outcome. Removed the spark plug again and kicked to see if any gas was spraying out, which there wasn't. Then I kicked again and again and it started. When it did start it was a very low idle that gradually picked up. If you gave it any throttle before the idle picked up it would stumble and die almost immediately. Also it would only start with the throttle completely closed. There was also a weird coincidence of if I either pulled in the clutch lever or turned my headlights on(Trail Tech X2) the bike would cutoff, almost like turning a key in your vehicle. I feel these were just coincidences and have nothing to do with the actual problem since it did not do this every time, but I could be wrong.
We got it started one last time and I rode back to the truck as fast as I could. Once back to the truck I killed the bike and started removing all my gear. I then tried again to start it and it was not having it.
I've been tinkering with it in the garage the past few nights after work and this I what I've done/found:
Cleaned Carb --- no visible gunk in carb (BTW I work at a dealership, that doesn't carry Kawi, so I have access to a great carb cleaner)--- reinstalled carb, bike still cuts out randomly
Replaced spark plug with new plug --- after idling bike for a while plug was not black nor brown but still looked new with a small amount of gas on it.
Ohm tested source coil of stator --- within spec
Ohm tested ignition coil --- Just outside of spec on primary side but I still had spark
Ohm tested CDI --- Many readings that were displaying open when there should have been resistance
To elaborate on the CDI testing I found that when testing the Black/Yellow wire, which is the one connected to the ignition coil, it was not showing continuity with any of the other wires that it should have.
What is strange here is if I follow the service manual pattern of negative lead on the Black/Yellow and positive on the other wire being tested, I get an infinite reading. However, if I switch these leads around I get resistance, but it is in Mega Ohms, which may as well be an open or close to it. Is there a one-way diode inside these? There were a couple other readings that were off as well, but this is the one that alarmed me most since it is part of the sparking system.
My confusion lies in the fact that if my CDI is testing bad, I should have no spark at all correct? I'm wondering if when I'm kicking the bike I'm creating enough of a jerking motion to make some sort of connection inside the CDI that allows it to function, until the connection is lost again or the bike is shut off. I don't really know what else to check at this point. My compression is on the lower end of the spec, but it is still within its specified range. I've seen other people on here have issues with the source coil that tested good when cold and bad when warm so I'm wondering if that should be my next step.
If this issue doesn't get sorted soon I may have to upgrade to one of our Betas we have here at the shop.

If anyone has any pointers for me I'd appreciate it.