Hey there, welcome to the 'Zone William!
As for that 450. Truely I'm no technician, but I own that bike, ('04 450) but I can tell you that the warning light you mention, the blinking "
R" while in Park, is a code/warning light. That light usually signals that the IDLE is too high, or more likely, he's revving the motor a bit high after he starts it.
Smoke: could be too much fuel in the cylinder during all this troubleshooting too, unsure. Still doing it?? Kodiaks have a habit of eating oil normally too, then, if you fail to check it, it'll bite you with a to end rebuild (

).
Judging by your troubleshooting, it sounds like you've eliminated the starter, and battery and that area then, correct? Kodiaks and Bruins are a bit notorious for going through batterys, and quite a few left the factory with a bad cell in them.
One more Kodiak thing to check too, if its an 04, (straight axle rear susp, not independent), be sure to check the rear "swingarm" for cracks!!! Circled in
RED.
[attachment=2316:attachment]
Mines cracked clean through to underneath at the moment. Just one more thing to keep an eye out for...
Good luck, hang in there, you'll get more replies here!
MGJ