A couple things come to mind.
1: Since you converted it to 12 volts, I'm guessing that it normally was 6 volts with a POSITIVE ground. Does it still have POSITIVE ground with the 12 volt set up? Chances are is that you may have the coil hooked up backwards. On a NEGATIVE gound, the power wire is connected to the + on the coil, and the points are connected to the - on the coil. On POSITIVE ground, the power wire is connected to the - on the coil, and the points are connected to the + on the coil.
2: I'm not sure exactly what was all rewired or whatever, but do you have some kind of resistor for the points? Or is it getting a constant 12 volts. Points only get BATT voltage at cranking, then they get roughly half the voltage through a resistor wire or resistor block while running.
PS, if the starter has permanent magnets inside, you'll have to stay with a POSITIVE ground on the tractor. If it has an electric magnet, then you can convert the tractor to NEGATIVE ground. The starter will still spin the right way.