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There should be a seperate coil in the stator for ignition, battery charging/lights, so I would say no, but not knowing exactly how the electrical system is set up I can't be 100% sure. The 1987 LT80 my son rode years back was electric start, ran a homemade headlight on it for a long trail ride, ran the battery down too low to restart after stopping for a break, but it ran fine until shut off, so evidently the ignition and charging circuits were seperate on that quad. A quick jumpstart from my quad, and it was running fine all the way back to camp (with the light off, battery recharged fine). Bogging down and dying after warming up could be carb related, low fuel flow, or electrical, a bad spot in the stator or wiring opening up as it warms up and expands. Does it start up and run good when cooled down? that may point to an electrical ignition problem.
This is a question that depends on a couple things:
1) How many pins on your CDI? Is it four, or five?
Four pin CDIs are powered off 12 volts DC. If this is the case, and your battery is total toast, and if your charging system is flat totally dead, then yes your quad could die as your battery voltage drop to nothing. WHen you jump a quad with a totally dead battery to a good battery, the dead battery charges a bit from the good battery. The good battery provides the large current required to start up the quad, and then after that the quad runs off the residual small charge on the nearly dead battery. Ignition system draw little power compared to the starter motor requirements, so the quad runs for a while before it dies.
If you have a five pin CDI then this is less likely (but see the next scenario). In this case the quad is running off AC power from the stator - completely independant of the battery - and the quad should run forever until you run out gas or you shut it off. Once you shut it off you need a good battery to get it started again unless you can kick start it, or have a pull rope. I think this is the scenario that 95Wolv was referring to...
2) Do you have an auto choke? Auto chokes run off auxillary 12 volts from the regulator, or the raw AC battery charge winding from stator (through a power resistor usually). Note this power source is completely independant from the ignition power for a five pin CDI as described above. If you have a defective charging system, and have an auto choke, it is possible your choke never comes out of the "enrichen" mode. In that case a cold engine will run fine, then get worse over five minutes or so, and run bad when the engine is warm. I don't think this would cause the engine to quit all by itself, but maybe there are other factors adding into the mix...