unfortunately the MSD system does not provide any external way to datalog. No way to pull info from it.I've been following along for a while as well, thought I would chime in. I did a megasquirt EFI conversion on my 1973 Land Rover Series 3 with the stock 4 cylinder. Total home brew.
Your description sounds like what I had with ignition issues. Specifically, tach signal to the computer. Initially, I didn't strip the wire correctly. Tach signal wires are shielded, and I didn't strip back the shielding. So a bad connection there. Then the spade connector that connected to my coil wasn't any good! So I experienced the same problem you did, randomly, no tach signal, no injection. Like you, had no problems for a long time. Then all of a sudden, cutting in and out. Over time the connection wiggled loose and that was it.
Also I had a couple of bad coils. When the car was cold, no problems but a few miles down the road, issues.
But yes, I think ignition is where you need to be looking at. I'd start by looking at all of your connections. Do you have a way to data log? That is what will help you determine where you need to look. When you have an episode, you can see what goes to crap.