If you start to experience regular problems with this, I would keep the voltage regulator in mind. I had a 60 once that I had constant issues with thinking it was the alternator or a ground wire, etc. Every time I had the alternator tested, it was fine. After months of frustration, it ended up...
Losing compression in multiple cylinders sounds like a head to block issue, rather than burnt pistons, rings, etc and you said you had the valves done. I assume the block was inspected at the time of head removal? Any abnormal smoke? Are you seeing any oil in the coolant or coolant (muddy...