A few days ago I sent an email to Sonex, asking for advice about what to do with the Primary ignition. I had thought that maybe when the original magnetron was hit by the magnet assembly that maybe I 'degraded' the magnet along with ruining the top magnetron, so I suggested to Sonex that that could be the problem. Kerry at Sonex responded and thought that that was unlikely and asked me to ensure the wiring was proper and the magnetron was grounded well. If that wasn't the issue, I should exchange the top and bottom magnetron to see if the problem followed the magnetrons.
I checked all the wiring and found that everything was just fine, so I proceeded to exchange the magnetrons. While a lot of work to exchange them, this proved that the replacement magnetron I ordered from Sonex was defective, directly from the factory. Fortunately, I was able to 'borrow' another magnetron from a fellow nearby builder. Once this mag was installed, the primary ignition worked perfectly. The RPM difference between the primary, secondary and both was maybe 40 RPMs.