The magneto is a stand alone system. There should only be 1 wire going from it to a kill switch, the kill switch grounds the wire to kill the magneto. If you do not have the correct switch for the magneto, the magneto will still work so long as the exposed end of the kill wire is not touching anything and you can just touch the end of the wire to the frame to kill the engine.
To start the tractor you need one wire going from the battery to ground and another going from the other terminal to the starter, this is the bare minimum it takes to turn the starter using a battery. I would highly recommend installing a starter solenoid and running a wire from the battery side of the solenoid to a button back to the small middle post on the solenoid so you can start the tractor when you are sitting on it. The starter on your tractor can move the tractor if it is left in gear and if you are standing next to the engine you can be ran over by the tractor. Please be careful when working on old farm equipment.
Since you have a magneto, you don't even need to use a battery to start the tractor, you can start it with a hand crank, again, make sure the tractor is in neutral before standing in front of it and trying to start it. If you do try using a hand crank, be careful, if the engine backfires it can spin the handle backwards and break your wrist or arm. The only time I use a hand crank is when I have the battery disconnected and I am turning the engine over to set valve lash.
I have seen pictures of alternators mounted on a length of steel through the original generator bracket, personally I would remove the old bracket by cutting the welds with an angle grinder, removing the broken stud, and install a proper alternator bracket.
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Today's Featured Article - 12-Volt Conversions for 4-Cylinder Ford 2000 & 4000 Tractors - by Tommy Duvall. After two summers of having to park my old 1964 model 4000 gas 4 cyl. on a hill just in case the 6 volt system, for whatever reason, would not crank her, I decided to try the 12 volt conversion. After some research of convert or not, I decided to go ahead, the main reason being that this tractor was a working tractor, not a show tractor (yet). I did keep everything I replaced for the day I do want to restore her to showroom condition.
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