D, after thinking about it more, and a little experiment yesterday morning, I think you are right. Maybe you can spot my error, but I'm still digging... I pulled the fuel pump fuse, stuck a brand new plug in wire 3 and held it against the fender while I ran the starter. I had a very bright, consistent, blue spark. I did not repeat the test with the plug that has been in the block yet. The plugs are whatever Autolite part the O'reilly computer said was correct for the Patrol. Maybe I should be using a different plug with these coils?
As far as coil dwell, I've been reading everything I can find to understand better how to figure out what it should be set to. Currently, it is set to the 3.5ms recommended in the Megasquirt hardware manual for the GM 585 truck coil I am using. What I haven't yet stumbled over is why they used to recommend 4.5ms. I have read that you want that dwell as low as possible while not affecting idle; even as low as 2ms. I haven't made adjustments to it since I have a blue spark in the RPM range that the engine is acting stupid in.
I've left spark advance to the fixed 10 degree setting, and let it use the default advance table. When I first got it running, I really thought it was running pretty well, only slightly misfiring, and the advance table made a huge improvement in accel/decel, but it still worked at static 10.
I still feel like I have configured the TDC point incorrectly, but I have done it three different ways a dozen times and always come up with the same thing, so it just has to be correct. When looking at the engine from the front, my crank angle sensor is around 11 o'clock and the timing mark is around 1. With cylinder 1 at tdc on its compression stroke, the timing pointer is very close to lined up with the left most of the three timing marks on the crank pulley. From there, I set my missing tooth to be 50deg to the right of my sensor; which puts the missing tooth just ahead of the group of timing marks on the pulley. That's supposed to mean that as the sensor reads the gap, the computer knows that the engine is 50deg before tdc on compression for cyl 1, and from there it can handle all of its timing. That 50deg number came from the Megasquirt hardware manual for an inline six engine. I keep hoping that someone knows a way I can confirm that I have this correct. The only test I have done is to hook the timing light on it, set the light to 10deg, and the strobe lines up with the same left-most (last mark to pass the pointer when engine rotating) mark on the pulley.
When figuring out the wasted spark pairs, I did some more of my own math, which might be totally wrong.
I said if the firing order is 1-5-3-6-2-4, and we are using three channels (A, B, C) to drive the spark:
A will drive the first and fourth sparks, cylinder 1 and cylinder 6
B will drive the second and fifth sparks, cylinder 5 and cylinder 2 (or 2 and 5)
C will drive the third and sixth sparks, cylinder 3 and cylinder 4
So you wind up with the outer two cylinders paired, then the next inside paired, and finally the center two paired. Diagram for fun.
coil-signal-wiring@3x-100.jpg
These HV leads all seem to be working, but they did come from a junkyard 90s model Ford car. I have a spool of lead wire, maybe I can re-use these connectors... I'll work on making new leads.
I think the mixture is on the rich side, and leaning it out does make for a better idle, but I'm having a hard time judging it because not all cylinders are firing yet.
I'm probably trying to use too many old parts that I don't know are in good shape, and I didn't know until later that I ran out of gas during my last test to see which cylinders were firing. So, it might've just been out of gas... Maybe I'll have more news this weekend.