Running rough, less power

[SuperJet-Dave]

2004 Superjet. Engine is running rough and seems to have lost some power on the low end (e.g. when trying launch a wave). The engine vibrates pretty good. It has done this for a while now. I tried to attach a video file, but the site wouldn't allow .mov files. See YouTube link below. Engine mounts and engine cradle are attached solid. I tried to tune the carbs with the low end adjusters and the idle screw. Helped a little, but still running rough, and still seems to have lost some power on the low end. Carbs were rebuilt last year with original mikuni rebuild kit. Put in a new CDI a couple weeks ago (for a different problem). Spark plugs are relatively new. New plugs made no difference. Both plugs have spark. One plug is blacker/wetter than the other (see pic). I have been meaning to replace spark plug wires/covers. Could this help?
Any other suggestions?
note: ski has pro-tec head, factory pipe, Coffman exhaust.
Here is a short video...

 

[SuperJet-Dave]

I swapped in the ignition coil and wires/boots from my 2001 Superjet, and really did not make much of a difference. This coil has the expected 4k ohms resistance between the spark plug boots. My other ignition coil has no resistance between the plug boots, but they seem to perform the same... rough vibrating engine.
When I was tuning it at the boat launch, some guy launching his boat said that it sounded like it was running on one cylinder. I don't have the ear for that, but he maybe on to something. Although it seems to start ok, and runs ok at the high end. Just getting a loss of power at the low end. Maybe 75% of what I am used to. It is still rideable. I would expect more of an impact if it was only running on one cylinder???
Found some other threads on this, and they seem to point to the spark plug wires, ignition coil.
I might get some brand new spark plugs, since I may have messed up the new I have with testing? I may get a new ignition coil wires/boots anyways, since my one wire is kind of beat. I am kind of out of good ideas. Any suggestions?

 

[SuperJet-Dave]

Put in new plugs and got new plug wires for the coil through jetskisolutions.com (jss and John, Cory did a great job and were super responsive!)
Ski runs better, just not certain it is 100%.

How can you determine if you are running in one cylinder? I watched both pistons move when cranking without the plugs in. Both getting spark and fuel (plugs get a little wet). What else do I need to look at?