Ok, so I pulled the cylinder head off, and I'm more stumped then I was before.  There's a little oil in the combustion chamber and I've got quite a bit of unburned fuel in the cylinder as well.  With the valves open, there is no noticeable play in the guides.  The valve seals look fine as well.   

I'm not sure if the oil caused the misfire, and as a result the unburnt fuel in the combustion chamber.  Or, I've got a fueling issue, and it's washing down the cylinder wall and allowing oil into the combustion chamber.

Does anyone know if a set of throttle bodys off of a 620 are interchangeable with the 900?  if so, I'll swap out the ones off of a known running motor and see what happens.

While you have the head off I would pull the cyl. and check to be sure the oil control ring did not get broken during assembly. Much easier right now.

The rings look fine, the hardest part was getting the correct orientation of the end gaps.

What year is the 900 swap?  Carbie or Fuelie?

The motor is a 2000, the harness and computer are from a 2002.

Not sure if the throttle bodies are the same.

Which ECU are you running?

The ECU is from a 2002 900.

Ok, so tonight I changed the throttle bodies, injectors, and regulator from a known running 620.  It didn't make a bit of difference.

The oil in the cylinder is clearing up, so that may have simply been the rings not sealing 100% initially.

This whole problem is especially frustrating since at about 2800-3000 RPM it sounds oh so good.   It revs quickly with no hesitation, feels smooth, and has no misfires or smoke to indicate any problem.

Just for the heck of it, I'm going to replace the fuel filter tommorrow.

The filter was really gross, and definitely the original one in the bike.  That however wasn't the problem.  It still very much feels like a timing problem, but unfortunately I don't have anymore time to work on the bike this weekend.

Just got done pulling the flywheel and verify the gears driving the timing shaft were timed correctly, and that wasn't it.

I tried asking the local Duc shops about looking at it.  One is a month away from being able to take a look, and the other won't touch it because it's not stock.

Where do you live?

Someone here may have another suggestion of a dealer or indie wrench.

Anchorage Alaska, my options are pretty limited.  I did talk with Mark at DucShop who suggested a TPS adjustment, and trying to record some air/fuel ratios.

Hmmm...Anchorage. Limited options indeed.   

Perhaps a sticky injector.
Maybe the ECU is whacked.

I wouldn't think it's an injector problem, as I've swapped throttle bodies/inectors/regulator.

Anybody got a spare ecu/gauge cluster/key set laying around?

Yeah, you swapped TB's, I forgot. 

Is it dead on one cylinder at low rpm, or both?
I'm thinking it's just dead on one, or it wouldn't start.

All your electrical connections tight?

Grasping at straws here...

Both cylinders are firing as the rpm drops, but if it gets below about 2200 they both cut out.