I'm a bit confused by the wiring harness illustrated in your last post as it appears to have a two pin socket with one wire possibly being an earth. The normal set up for a Magnetron coil is one wire from the blade connector on the coil running to the engine stop switch on the throttle plate. That said, the coil in your post is unlike any BS coil that I've seen, but as four years have passed since retirement, perhaps things have changed. None of the wires that disappear under the flywheel are needed with a Magnetron coil but it may be easier to either disconnect the stop wire from the old condenser and take it straight to the blade / spade connector on the new coil or cut it off close to the points enclosure and do the same.. That way you don't have to make any changes at the stop switch end.