old_thumper

...if the battery is hot there could be another issue in addition to the neutral switch going bad. I would also check the cables/connectors to the starter. You may have a bad cable/connection or bad ground. This may have been part of the cause for the neutral switch to go bad...

...if you have a bad ground connection or a bad battery cable, it can cause this. Did you check the starter connections & battery terminal connections? I would check the main fuse again & maybe replace that housing. To be sure you could take the whole wiring harness off, clean all connections and put it back on the bike. Then before connecting the positive battery lead, do the groundhog test. >turn your back & connect the wire to the terminal- if you see your shadow you have 6 months more work to do

..also before doing an Ohms test check all switches & connectors for continuity. Make sure that there is enough voltage coming from the battery system (approx. 12.8v). After testing lights switch, engine stop switch (kill), starter switch & main switch do an Ohms test . I think that this will work for your bike but not 100% sure. Ohms testing with meter: Disconnect the coil connections from the wiring harness & connect to meter. ignition spark plug gap = .8-.9mm or .03-.04in main fuse = 20amp primary coil = (+) orange to terminal (-) ignition coil base >> (Ohms x 1) primary coil = (-) spark plug lead (+) ignition coil base >> (Ohms x 1K) primary coil = approx. .18 -.28 Ohms (at 68deg F) secondary coil = approx. 6.32 -9.48 Ohms (at 68deg F) pickup coil = (+)red (-)white approx. 450 -561 Ohms (at 68deg F) charging (source) coil = (+)brown (-)green approx. 270 -330 Ohms (at 68deg F) lighting coil = white-white approx. .702 -.858 Ohms (at 68deg F) Disconnect magneto connector from wiring harness (check all 3 wires) stator coil CDI= (+)white (-)white approx. .702 -.858 Ohms (68deg F) starter motor armature coil= approx. .025 -.035 Ohms (at 68deg F) relay coil= approx. 4.18-4.62 Ohms (at 68deg F)

...I know this may be an obvious thing to check, so just wanted to note: I have chased strange ignition issues in the past to find that the "kill-switch" was shorting-out or that the main switch (key) was failing. Testing these switches with a multi-meter is pretty easy. Another obvious thing to check is the battery terminal/starter connections.

before pulling the carb off try draining the fuel tank & the float bowl completely empty. then refill the tank with premium gas & seafoam addative (or any carb cleaner/snake-oil addative). leave the float drain open until the gas looks good and then replace the float bowl plug. remove the airbox cover & filter (making sure the box is clean before removing the filter). then spray some aresol carb-cleaner (not ether or starter stuff) into the intake and turn the bike over until it runs for a bit on the carb-cleaner. if you can't get it to take then the carb needs to be removed/rebuilt.

...thanks for that link. The service manual he has is for a '98 600 YFM. I have seen one for an '01 at one time and was hoping you had one for me.