I wanted to write this up so others who are having the same problem can save the hours & dollars I've spent trying to figure this issue out.
The Problem: Rarely, most noticeable on colder days and only when the bike was completely cold, the starter would suddenly die while trying to start the bike. It acted almost like the battery was bad, releasing the starter button and trying again would have the engine crank over a couple of more times and then usually die again. On the third try the bike would start (after a bit of complaining)
The Troubleshooting: I'll try to keep this simple/short
-Checked battery cables
-Replaced the battery (sitting voltage was something like 12.3v, battery was 3+ years old)
-Tightened cable on starter
-Checked relay (under the seat)
-Checked starter solenoid
-Checked all cables (button to relay, etc)
-Replaced relay (Service Manual states that when you short 2 pins, you should get the battery voltage on the 3rd pin, I was only getting 90% of the battery voltage, the new relay did exactly the same thing... thanks Kawasaki...)
-Replaced starter solenoid (just because I was running out of potential sources of the problem)
-Checked the starter
-Replaced the starter (less fun than it sounds)
-Cleaned the starter button
It was at this point I was stumped, the problem was so intermittent it was frustrating to troubleshoot and several times I thought I found the issue to only have it crop back up 2-3 months later... Until the issue was happening regularly one night and I wanted to prove the point that you don't need any electronics (no ECU, no PCV, no ignition, lights, etc, etc) to simply crank the bike over, which to re-iterate, is what would stop working (of course the bike won't fire up without the ECU, but I just wanted it to crank).
So, I unhooked practically everything except the 2 cables from the battery, the relay/solenoid and of course, the bike cranked like it was going out of style. I hooked up my various electronics, specifically, the PCV, ignition module, auto-tune, heated gear lead, trickle charger lead to the common ground on the bike. At this point I tried to start the bike and low and behold the starter just died.
Now... I've installed many car stereos & car phones and I know the best ground is to clean metal on the frame and a common ground (google ground loop oscillation if you don't believe me), so naturally I used a wire brush and cleaned this ground before I started. I also had tried slightly longer bolts and using a washer to make sure I had great contact and made sure that everything had a good ground...
So, I had an extra piece of heavy gauge wire from my replacement starter and I hooked it up to the battery's negative terminal, ran it out of the battery housing and connected all of my aftermarket parts using a simple nut and bolt. For the last 4 months I have not even had a hint of the starter dieing.