when I turn my key to magneto it starts missing and runs rough I put a new mag in
Are your coils expertly tuned up Paul? Plain old every day coils just won't give you the performance that a set of coils will that have been rebuilt properly. Most people think that coils are just coils, and that contacts are just contacts and there's nothing fussy or important about them ...
If you have a friend who has a T which runs good on magneto, borrow his coils and try them in your car. If that fixes the problem, you need to rebuild your coils.
Have you checked the output of your magneto? It should generate from 6 volts AC at idle to nearly 30 volts AC at high speed. Use an analog voltmeter. There are other posts which describes exactly how to measure with a light bulb in parallel to the volt meter.
If the voltage is low, the magnets need to be charged and or ring repaired or replaced. With the voltage low, rebuilding the coils will not help.
Another potential problem could be your ignition switch. Try reversing the wires between battery and magneto on the switch and see if the engine still runs on battery. But don't accidently connect the battery to the magneto or you will discharge the magnets. If it still runs good on battery but not on magneto, the problem is not in the switch.
Paul, was the magnets recharged and the gap set from .025-.045? if yes then I would say it is coil issues, another trick to try is after it is warmed up take your mag wire and go directly to the coil box to rule out a bad switch, I have had a couple that the switch was shorted out.