Well............... who knows. (since I'm not there looking at it) You could have a bad wire... or a weak coil. Besides... these engines don't run well on one cyl anyway... so it's not really a valid test for anything.
Put an in-line tester on both plugs at once, and see what you get.
A miss in the mid RPM's could be anything. It's a 2-stroke... and since you were on the trailer... the engine was really loaded up, and it's really not tuned for that. Yes... it's best that you test the engine in the water, as you were doing... but once past the "Check for leaks, and other issues" stage... then you really should just get on it, and take it for a ride to see if it clears out. My personal XP needs 10~15 seconds as I get on the throttle the first time to clear out. (can't do that on the trailer) But once clear... it's fine the rest of the day.
One last thing... the Mikuni carbs don't have a "Mid" fuel circuit... so some of these engines just run that way. BUT... if your RAVE's are opening too soon... that could cause the loss of power in that RPM range. I personally run mine full tight, so they don't open until almost peak RPM's.
Last thing... if your water regulator isn't set right... or is leaking... then that will cause a mid-miss also.
9 times out of 10... if it was an ignition issue... then it would feel like it was turning on and off... not just a miss.
Just my 2 cents... take it for what it's worth.