This might help someone else:

I was working on a 2008 Polaris sportsman 800 HO that was swamped. IE flipped up side down in the water.

It had low compression, and would back fire and burble but was very hard to start up when cold. it ran OK once warmed up though and this was the puzzle.
Code 21 Engine sync.

We found some burned wires on the TPS sensor so changed that out.
Went through all the wiring checking for bad connections, shorted or open wires, using a multi-meter but found nothing.
swapped out the CPS, ignition switch, Coil, installed new plugs and Wires.
swapped out the TBAP sensor, and the ECU. everything worked great on the donor quad.
replaced both injectors, one was iffy. and checked fuel pressure and flow, 39 psi and good flow.
Then replaced pistons, and changed out exhaust valves which we're warped enough to hinder sealing and I believe was the source of the back firing. I then checked the flywheel keyway and the counter balance keyway, both we're good.
bypassed the throttle safety switch, and the engine kill switch. all to no avail.

Then I put an engine timing light on it, tied the trigger up so the light would always flash, and noticed that it would flash steady until the engine fired and RPM's climbed up to about 500. then suddenly no flash. and the engine would die. again Code 21.

placed a pry bar against the back of the CPs and pried it against the casing towards the flywheel and the engine fired right up.

I then measured clearance, and found I was at .79" and was supposed to be at .59". So ground off .020 from the casing under the CPS to move it closer to the flywheel. and voila. it runs like a top.
I've never heard of this, nor found any answers on any of the forums, so hopefully the timing light trick will help others.
sincerely
Smokyash.

 

The timing light method has been around a long time to see if spark is breaking down,used it several times myself on finicky problems. I like how you solved the problem on the cps gap! If it doesn't have the correct clearance,alter the case a little until it does. Glad you got it going,sounds like you had your hands full!