Start with the easy stuff. You rode through a sandstorm so check your air filter (unlikely cause since the other cylinder is firing but it wouldn't hurt).
Air filter is pretty dirty, even blew a bunch of sand out of the frame while I was checking it. I was also thinking it was an unlikely cause due to the other cylinder firing as you mentioned.
Check the ground connection at the frame. If there's more than one, check them all. Just because your battery connections are tight doesn't mean the other end of those cables is as well. Definitely doesn't mean that your ground cable isn't corroded to hell from all the water, dirt, etc you rode through.
I measured 0.2-0.3 Ohms at the ground at the front left of the transmission case as well as the one at the rear left near the clutch cable hanger. I think 5 Ohms was the FSM max reading. I'll have to see if there are other grounds to be tested.
Pull the spark plug, is it wet and smelling of fuel? If no, you're not getting fuel and you need to start at the injector and trace back until you find the fault.
Plugs looked good when I pulled them initially and when I pulled them after getting my bike back. At that time however, they had only run on one cylinder for a couple of minutes followed by 400 miles of proper operation leading up to my no start issue. That probably cleaned them up. They may very well be fouled now after tinkering with the fuel map in my garage and going for a brief test ride. I'll have to re-check them.
If yes, are you getting spark? Lay the plug against the cylinder head and crank the motor, you should see a big fat blue spark. If no spark, or spark is small, faint, or yellow, you have a spark fault, start at the plug wire and work your way back until you find the fault.
I did this test while stranded at the gas station. Saw a blue spark on both plugs, but can't say for certain if they were big and fat. I've only tested plugs like that one other time (on a lawn mower) and after shocking the crap out of myself on the front cylinder, I was a little gunshy when checking the rear and only cranked it once. I don't really have much past experience to compare my observations to.
With new wires and an ignition coil that was confirmed to be good by the dealership, what else is there? ECM directly supplies the ground signal to tell it when to fire, correct? Continuity test between the ECM plug and the ignition coil plug? I guess new plugs probably couldn't hurt.
If you're getting fuel and you're getting spark, the next thing I would do is a compression check
I think that's next, should have grabbed the compression tester while I was at the auto parts store the other day. Hope I haven't toasted a cylinder somehow...
if that checks out good I would find someone willing to loan you a known good ecu and swap that out just to make sure yours isn't toast. If that still doesn't work, start testing all your engine sensors (dunno what all sensors our bikes have but cam and crank position, intake air temp, map/maf, etc. are all possible causes of poor running if one or more are bad)
In the FSM, it basically says the ECM is the least likely thing to fail. Something like a 0.1% chance of failure. At the end of the troubleshooting flow chart when it gets to the ECM, it actually tells you to go back to step 1 and repeat ALL test procedures a second time before beginning to suspect the ECM. That being said, mine has been rev-extended by Lloydz, but it appears to be in good physical condition (no bent pins, no sign of dirt or moisture in the connector).
As for the sensor tests, most of the tests seem to require either the Digital Wrench and/or a more advanced multi-meter with special probes to poke into the harness connectors. I've got some connector pins from another project, maybe I could make myself some probes? Visually inspecting the connectors probably wouldn't hurt either.
Thanks for taking the time to reply. I'll take your adivce here and hopefully it will help lead me to my answer.