Small Engines (Lawn Mowers, etc.): small engine repair, throttle shaft, belts and pulleys

Question
hi, I have a simplicity regent hydro with a kohler command 16 hp. model cv16s serial 2822220431 family skh42641g2rb. i have owned the tractor for 2 months and it has ran fine but the last 2 times ive used it, the rpms will suddenly drop and the engine will backfire 1 or 2 times rapidly with a puff of black smoke. sometimes it will die sometimes it wont. if it doesnt, i shut it down anyhow to be safe. it starts easily and runs and sounds fine at first but its to the point now where it does this after about 5 min of running. it makes no difference if the electric pto is on or off. dont know if it makes a difference but the battery is dead and i have to start it each time with a jumper pack. i didnt have this problem till the battery went dead. i also have another problem but i dont think theyre related. the same time this started happening the electric pto started acting up. sometimes it wont engage. i can hear it click and try to engage but blades will not turn. mower deck belts and pulleys are free. i was just assuming the clutch was bad bud maybe the two are related? hope i gave enough info. i greatly appreciate any help you can give. im am mechanicaly inclined but i just dont want to chase the wrong problem. fuel, spark, ETC. thank you very much.

Answer
I have seen some Kohler's do this.  Have you cleaned the carb and check the throttle shaft for wear.  Check/clean the valve breather.  The puff of black smoke is telling you it is running too rich.  FYI, these are sometimes the most difficult problems to solve.

How old is the mower?  Do you have a volt meter to check the charging system.  I do not think the two problems are related but it is possible.  Is there any wires connected to the bottom of the carburetor?  How old is  the battery?  Dis-connect the battery and clean the battery posts and cable ends with a wirebrush.  Then charge the battery.  It would be worth you time to have the battery load tested at you local autoparts store.  

At this point you are just ruling out the easy things.  I have fixed a lot of weird problems just by cleaning the battery connections, carb and valve breather.

Let me know how old the mower is.
Eric