I've been digging through the front harness looking for crossed wires and realized there's actually not a problem between those two wires. I hadn't removed both relays (2 and 4) when checking for continuity between the 60 amp fan fuse and the green/black ground trigger wires for the fan relays. So basically it's the same problem I was having with the fuel pump relays. I had swapped in a 93 front harness in place of my 94 harness 3 years ago, and the 93 harness has the relay coil wire run to the 60 amp fuse, which goes to the battery positive, whereas the 94 harness has that wire going to the ignition switch instead. So it's exactly like the issue with the fuel pump relays I had to rewire. I'll be swapping back to my old harness this winter.

I got the new coils but haven't swapped them in yet. I'll probably do that when we get back from our vacation.

 

I swapped the coils a couple weeks ago when they finally came in and took some logs that night but didn't get a chance to look until we got back from our two week vacation Sunday night. It looks like the problem is still there just going based on trigger tooth count. So I guess it could still be the flex fuel sensor being wired to sensor ground, maybe a bad CAS even though it's new, a corrupted tune, or maybe my engine is old and worn enough that the end play is causing the trigger wheel to move far enough from the sensor while the engine is turning.