BF90 missing below 2500rpm

"I have a 2006 BF90, less than

"I have a 2006 BF90, less than 20 hours. In spring it started perfectly. Within 15 minutes of running it started to run rough and then died. I could restart it with choke and it would rev but struggle and cut out until I repeated. Eventually, it idled rough and I got where I was going. It ran better at higher RPM but still cut out a few times.
Since then, it starts fine and runs great above about 2500 rpm, but sounds like it's intermittantly missing a cylinder below that. I've run 10 gallons through it with some STP type carb cleaner and put new gas in, same thing. Next time I get to it, (it's 250 miles away) I'll pull plugs to see if it's just one cylinder.
Although I used fuel stabilizer last fall, is it possible this is some gunk in a low speed jet on one carb? How big a deal would it be to get it out if that is what the problem is. I'm on my way to get a shop manual.
When this thing ran last year it was quiet and smooth."

You need pull off all the carb

You need pull off all the carbs and clean them out. You have one or more clogged idle or mid-range jets.

"Ouch. Thanks (even though

"Ouch. Thanks (even though it sounds like a royal pain).If I knew I'd be doing carb removals after 20 hours I wouldn't have bought a $10k new engine, a 20 year old clunker would have been equivalent. Whining aside, do you think I can guess which cylinder it is by looking at the plugs (so I don't have to do all 4)? Also, the engine stumbles in and out, running smoothly for several seconds at a time, and alternates back and forth. Does this sound like varnish or some small solid particle? What would make a jet open up and then close; why wouldn't it stay plugged?
I'll consult the manual when it gets in, but is this a big job, i.e. are the carbs & linkages tricky to get off? Will I need gasket kits etc?
Also, for the long term, I'd appreciate any suggestions on the best way to improve Honda's filtering so this doesn't keep happening. This has a new tank, all new fittings and hoses so there is no rust or water. I'm surprised the honda fuel filter wouldn't catch stuff big enough to plug carbs."

Welcome to the world of 4 stro

Welcome to the world of 4 strokes and higher maintenance costs.But having said that you should run the fuel out of the carburetors any time you take the boat out of the water or is going to sit for a long time.Fuel today goes bad much faster than it did say 30 years ago.