Prior to the 1/4 cutting out I had tested the coils by swapping and the problem stayed at 3/4 (at the time), this leads me to believe it is not the coils because of that. They're correctly routed right now.
Spark plugs look wet - I know all 4 cylinders have fired up in the last 48hrs at some point. Makes me doubt its a fuel issue.
Could the problem be from overheating, running too rich and not moving for 3min?
No, overheating takes much longer than that.
If the coils are the old OEM type by TEC: they are known to give up at some point. About half the time they 'die' by having erratic output at temperature, usually about 1/2 of normal spark output. I have seen it in the OEM coils several times, and in the Dyna green 3-ohm coils many times.
The failure mode is: the varnish-coated wire that is used in these units has a limited life, which is accelerated somewhat by heat. In the case of the 500/550, the configuration of the fuel tank is just right that they get little cooling as the airflow is mostly blocked, and they sit right above the engine, close to the exhaust headers. That's a LOT of heat. Once the varnish breaks down on the wire(s) inside, the tiny air space between that wire and the next one in the winding gets squeezed to 0 distance when the coil is hot, but has some distance when cool. So, the coil measures OK at room temperature, but when heated to about 150-180 degrees (F) the windings short out in several places.
I first discovered this characteristic in 1978 after my brother's CB500 did this to one of his coils at 45,000 miles (and 110 degrees while crossing Kansas i August that year). Poor guy...we has just finished touring the entire US Southwest for 3 weeks (I was on my 750) and after we returned here to Colorado, he went back to Missouri on his own. But, at about Wakeeney (on I-70) the 500 suddenly dropped to about 40 MPH top speed (his 500 could run about 107 MPH top end), backfiring and smoking. Each time he pulled off at a freeway ramp for a few minutes, it would straighten up again after stopping the engine for 10 minutes (in the famous West Kansas winds, typically 40 MPH). He would then hit the interstate again, and in 3-5 minutes the trouble would erupt again. He bought new points at one exit, a whole new points plate at another, camping and installing them at that Kansas exit each time overnight. He finally limped home that way (central Missouri) and when he got home he bought a new 1-4 coil: problem solved immediately. I got his old one to do the testing, to figure out the failure mechanism.
