My M109R stall when I put it into gear, The stand switch is plugged in and seems to be working correctly. I just installed new air filters and a fuel processor. Runs fine in idle.

Kick stand safety switch, try it after putting up the kickstand.

Could be fuel filter,air filter,dirty throttle body.

Even though you drained the fuel it sounds like the carb needs to be cleaned or else the diaphragm in the carb may have a hole in it. Can you pour fuel in the carb and have it run so it is the carb. Hope this helps. In addition, did you gap the new plug sometimes they get closed up in shipping.

Most probably, the AIC stepper motor is bad, one way to kno, is when the engine slows at idle when you swithc on the air conditioner, and the Idle automatioc control does not correct the RPM dropping from the increased load. An engien that does not maintain correct and stable idle cannot maintain the battery charged, but it could have multiple issues.

Have the fuel pressure checked if it is weak,it will cause this .

Stalling is normally caused by a problem with
A) Lack of air - check your air filter
B) Lack of fuel - the fuel filter/fuel injectors get dirty
C) Lack of spark - inspect your plugs & wires
Might want to try cleaning the throttle body. Every 30k miles they should be cleaned.
Best bet however is to take it to a reliable, licensed mechanic. Vehicles 1996 & newer can have diagnostic codes read by a computer hooked up to the vehicle, identifying the problem.

The tps has to be set properly to work correctly with a volt meter or scan tool.

Yes, yes, and yes. Begin by installng new spark plugs. Also, a new air filter, and finally put carbeurator cleaner into your fuel tank, usually one ounce per gallon. You can purchase these items at any auto parts store. Bring the old plugs and air filter in so u are sure to get the correct ones. Finally, charge up your battery.

I Have Started lots of Motorcycles that peopel have even thrown A way.
The most problem is with the carb or electric.
This what I have been starting bikes that A pigs to start for my last 28 years of Motorcycles.
Even with kick start bikes can build compreshion and kick back.
This can realy tire you out too.

1st wiggel all of the wires check for burn marks.

2nd Fuse box check for correct ones have been put in.

3rd Spark Plugs just put in new ones low cost cost for brand new .Check to see if You have Spark
if you don't Get A tester And read the service papers .

4th most of the fuel is years old trust me you need to mix 25/50 of Avation with super TT olny with yamaha RD 350 .You have penzoil for two strokes stick to olny one .

5th Fuel line pull the whole lot out put a air hose down blow it out .Clean fuel filter down the line
Clean the Air Box

Warning some bikes dont like Engine start Some with YPVS..
Playing with the enging iddl switch is not realy recemeded if the Bikes Not Runing !.
The Center stand could be down some bikes don't go with the center stand Down ( Its a safty Thing )


Turn the fuel on wile clutch out this will un block a air lock in the fuel line
6th Look for the Steepest hill you can find ! Stick it in top gear And wile you Speed up Like Really Fast STAND UP ! And push your weight on the foot pegs .And Repet this you should be clocer in starting to 3rd Gear if not 2nd .Pull the clutch in If you Its just Getting The fuel in .
If theres fuel in your Glass filter your on the way.
The twist grip Throttle A boult Half OPEN And when its Splutting coffing Give it the berrys.Chears From Rd 350 (R) with 77 owner

Its really sounds like the throttle switch, chack him.