Does it run at all now?
Can you run a vacuum check? It will tell you a lot about valve condition and possible manifold leaks and timing issues.
When you purchased it from the PO how many miles did it have on it since the rebuild? -
Could the cam not have been broken in correctly and you have a couple of lobes (6&7) that are wearing and causing issues?
When you began to notice issues was it after you returned from a trip? if so any time that you noticed the performance degrading after filling up with gas?
Any back firing? I have a friend that had a back fire from a carburetor that was running rich and it caused the intake manifold gaskets to blow out in several places, which caused idle issues. If it runs now you can check for cracked gaskets with WD40 or the like. Just spray it around the manifold gaskets and if you can detect the engine speed up or smooth out when you spray it you can locate the source of the leak.
Since it was running well ( no smoke at idle, under load or deceleration ) I would not think it was a ring issue, which leaves valves, carb and ignition.
Valves: bad gas (contaminated by water etc.) could cause burnt valves. You have covered that with the rebuilt heads ( did it ever get hot?) Did they check (Pressure and Magnaflux) for a cracked head or a cracked seat that would only show up when the engine is at operating temp and expands due to the heat otherwise.
Ignition issues - lots to cover but start with basics - fresh plugs, check cap for carbon tracking inside cap and check for cracks inside and on towers - rotor - in phase and contacts clean, check inside that goes over the distributor shaft to make sure it is not cracked or wallowed so that it remains in-phase
Wires - different ways to check but can be tricky to find an intermittent short.
Carb - issues - which carburetor are you using?
Timing Chain and sprockets - check play
Distributor - check vacuum advance diaphragm and make sure that the advance plate is free and working correctly.
Man this looks like a bunch to do but most of it is really simple and can easily be done by you.
Here is a link to the rocker shaft shims:
http://chucker54.stores.yahoo.net/rocshafshim.html