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...
In addition to ^, and to make sure there isn't a problem here, grab the drive shaft at each neck next to the u-joint and shift it up and down to see if there is any slop in the u-joint. And...since you just went to the shop, make sure the drive shaft bolts are snug too!
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...