I think the main problem here is that you are just replacing parts instead of troubleshooting the problem logically. You already know WHERE the problem is (#1 and #3 plugs); you just need to figure out WHAT it is. You say you have new wires, so, you are ruling them out, but it wouldn't be the first set of defective wiring sent to a customer. You need to look for arcing around the distributor, high-voltage wiring, and plugs (easiest in the dark), try new wires for those cylinders, take a close look at the contacts, pull the plugs and make sure they are not fouled, and try new ones anyway. Messing around with timing or unrelated things like the voltage regulator is not likely to help; they just don't affect what you are seeing. Similarly, if the coil were bad, it would affect all the plugs, not just #1 and #3. So that is not likely to be the problem.
The fact that it runs OK and suddenly starts to misbehave implies that there is a bad connection, or something similar, which gets broken and reconnected accidentally as you work on something else. Look CAREFULLY at the connectors at both the cap, and make sure they are getting ALL the way down into the hole and making good metal-to-metal contact. Do the same at the plugs; make sure there is tight metal contact. Pull the #1 and #3 wires and make sure you are getting a strong spark to a ground point; if so, the wire may be OK and the plug bad.
Once, when I had a similar problem, it turned out that the DPO had used the wrong connector for the center of distributor cap, and the wire was just barely contacting the metal connection in the cap. That's the kind of thing you are looking for