Hi, I have a Cub Cadet which had a 16hp BS motor with points. It went bad so I found another 16hp BS that does not have points, it has the magnetron ignition. I am having trouble getting it to fire, is there something that I need to change to the wiring to make it fire. The magnetron engine came with the coil.

Not really, the newer magnetron coil is just two wires, the spark plug of course and the kill wire. Was the engine new? It could have had no spark all along from a bad coil, but pull that kill wire off and try it then, make sure (this side out) is towards you, and the coil and flywheel are clean and gapped at .10