Ah shit. I've got the opposite problem with my RF900.
Runs on three at anything less than half throttle. Then takes off like a raped ape. And it's not the first time. I've already replaced the jet needles so it must be something else.
Lets face it guys, the Mikuni carbs on these bikes are a liability. I'm not too sure how much different 400s carbs are to 900s, so I'll give advice based on the 900 (so I could be completely wrong here).
First point of call could be to drain the carb bowls. Then pull the bottoms off and unscrew the main jet. Blow some compressed air through the sucker. Check the jet needles - there could be excessive wear there. In fact clean out all the jets you can get at and unscrew. And change the spark plugs while you're at it.
Then reassemble and test ride the bike. If its still not pulling it wasn't blocked main jets.
Then start looking at the coils. A good way to isolate coil problems (thanks Frosty for this tip) is to swap around the coils. If No 1 cylinder ain't working right (you can tell - after a short ride at reasonable revs the header will be colder) swap the coils around so that the other coil provides spark to the no 1 plug and try again. Problem persists - it ain't the coil.
After that it could be worth looking at blockage in the fuel hose, or the fuel pump itself.
Very unlikely to be the CDI. They either go or they don't.
And I to my motorcycle parked like the soul of the junkyard. Restored, a bicycle fleshed with power, and tore off. Up Highway 106 continually drunk on the wind in my mouth. Wringing the handlebar for speed, wild to be wreckage forever.
- James Dickey, Cherrylog Road.
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