Engine - Drivetrain

Gear indicator on the dash indicates every gear, so I don’t think there is one.

Well the shifter you use on the left side of the tank shifts N, L, D, and R.  That's it.  All of those associated gears are under the rear engine cover.   The actual transmission on these Rubicons is a hydrostatic unit, so it runs off of oil pressure.  Yes, there is a shift motor, but all it does is move the swash plate on the hydrostatic, so what you have going on is something either in the mechanical linkage between the shift knob and the engine, or something under the rear engine cover in the shift drum and associated drive gears.   There are some pics in this thread.   Third post down shows the gears on the back of the engine.  When you shift from N to D, L, or R, that shift drum turns, and moves the shift forks, which engage the appropriate gear.     This schematic shows the shift shaft and how it engages that shift drum.   https://www.partzilla.com/catalog/honda/atv/2007/trx500fga-2a/gearshift-fork-gearshift-drum   So the shifter turns that shaft, which runs all the way through the engine and turns the drum under the rear engine cover.   I actually have to pull the rear cover back off of one of mine.  I went through the engine and must not have gotten something together quite right as I only have 3 gear positions and when the machine shows Neutral it tries to move forward.  I think I must have gotten a gear backwards under that back cover.     But do you understand the general concept now?  You move shifter, shifter linkage turns that shaft in the schematic, which turns the shift drum on the back of the engine.  The shift drum moves the shift forks, and makes the proper gears engage each other. 

did you locate the diode in the wire harness ( i am not sure there is one ? ) if this diode is bad ?, you won't get power to the gear position switch.

no worries bro. i do know for a fact ( been doing this over 30 yrs )..that only ONE wire that goes to the gear position switch, most times this is a green/red stripe wire ?, that when you turn the key on ?, this wire becomes '' hot ''. sooo..when you shift out of neutral to any gear, then the switch tells the c.d.i./ecu/ the control unit its no longer grounded, which then turns the neutral light off on the dash. when you go back to neutral, you then ground the switch, then the light on the dash turns on. i'm not as fancy with words as retro ^^^ ?, but i do understand how the gear position switch works, been down this road for over 30 yrs..its something i've learned in this time..lol.

Welcome! What specific electrical issue are you having?