No I didn't mean the hydroststic transmission ... I meant the shift control motor ,this motor changes the angle of the swash plate inside the hydrostatic transmission ..The different angles of the swash plate is what changes the bikes speed ,there are no gears in the transmission..
In the "connector location" page #4 you will see where the "control motor 2p natural" is .. this coupler is for the shift control motor..
Has your dealer had many of these motors apart .. They are not the easiest to work on and you can't buy replacement parts.. We've taken apart dozens at our shop that Honda Canada wanted cleaned to fix a "lazy shift" problem ..
Anyway yours should be un-plugged and try another fuse .. Yours doesn't really sound like a dirty motor ,it sounds more like the shift control motor is seized or has a short in it ..
Try un-plugging it and here's section #24 from the 2004-06 Honda TRX400FGA PDF shop manual ..
When you get this fixed the bike must be re-initialized and the speedometer calibrated ...