O K, so after reading the Pro RMK service manual, studying the wiring diagrams, and with some help from a couple guys on this site, I think I may know how my sled will be fixed.
One guy with a '13 pro with a turbo replaced almost every electrical component on the sled and turbo kit and finally found the culprit. A bad fuel pump. It was pulling over 8 amps. He put in a new one and it pulled shade over 6 amps and his sled ran perfect. So i decided to check mine. It was pulling around 6.8-7.1 amps hooked to a battery that was at 12.25 volts. Not real bad. (I found the pump pulls more amps as the voltage goes down) So then I tried testing the voltage that the pump sees when I start the sled. When I started the sled it would only see around 7.8 volts at idle (1700rpm+or-), then when I gave it a little throttle it jumped to 12.5-12.8. I let it warm up and shut down, restart, shut down, restart, ect. Some times it would stay at 7.5 volts and sometimes it would go to 12.8 volts on start up. After warm up my idle was 1900-2100. So i think at elevation it probably doesn't idle as good and will idle lower increasing the chance that my voltage will be lower and stay low until I give it throttle to make it come up to 12.8.
Then I decided to unhook my AEM o2 sensor and checked for the amp draw on it. It checked out at 1.2 amps at peak. Then I unhooked the oil pump for the turbo and checked that. It was pulling 1.8 amps. Then I hooked the oil pump to a battery, left the o2 unplugged, and fired the sled. Bam!! 13.6 volts. Shut down, restart-bam! 13.6 volts.
So it seems that my fuel pump, while not too bad but slightly high amp draw, along with the o2 and oil pump has enough draw to make my electrical system have fits.
So I have a small 12v 4.5a/h battery, a painless wiring/fuse block kit, and a Polaris electric start harness coming. Another fella on here gave me the heads up on this mod. All my turbo electronics will run off the battery and the battery will be charged by the lighting coil/battery charge circuit.
Should have it installed next week, so we will see how it pans out......