This looks to be a mistery issue that takes a lot of head scratching to solve. I've had a few of them I will describe below. None of them correspond directly to your symptoms, but it may give you some ideas.
I had a similar issue on a W109 6.3 where I was loosing spark to four cylinders when the engine was hot. Eventually spark would disappear on all cylinders. The culprit was a wire connection to one of the two sets of points. When the engine was hot metal was expanding and the connection was too close to the distributor flange and was ending up touching it. As a result that set of points was grounded leading to the loss of 4 cylinders. After a while it was grounding the whole system and the engine was stopping. In your case we could imagine a similar thing happens but only at a certain position of the shaft relative to the flange (in case you have a bit of wobble in there) leading to the loss of the two cylinders corresponding to the lobes on the shaft in a given position.
Another issue that took a lot of head scratching was the wire that goes through the distributor (or the connection you have there) is damaged and you also have some grounding happening there. But you would be loosing spark on all cyliders.
More recently, I had two HT wires crossfiring because they were next to each other while spark was on two consecutive cylinders. Spark was jumping from one to the other wire leading to misfiring. This happened on an EDIS ignition which is much more powerful than the one you have, but you may try to run the wires as distant as possible from each other and see if your problem is still there.
