If you haven't already, check out page 45 of the Aerovee manual:
http://www.aeroconversions.com/support/ ... Manual.pdfIt's not clear if rotating the magnet cap 180 degrees was just a guess, but the manual will confirm whether you have it correct now (by comparing to the primary ignition magnet).
I don't recognize the yellow wire you mention. I think the old triggers had 3 wires, one of them being orange. The new triggers seem to only have two. Because of this, I can't really comment on whether your measurements seem correct. Also, I think these sorts of measurements can be tricky because the triggers go to sleep after a little while if they don't sense the magnet. You should measure ~12v across the low voltage coil and see it drop near 0 when triggered. I can't remember if it stays 0 while the magnet stays near the trigger or it returns to 12v after a few milliseconds. It's certainly too brief to measure with a multimeter on a running engine and possibly also impossible when turning by hand. I've measured it before with an oscilloscope.