Unfortunately, I have to assume that the machine shop that did the work did a proper balance job. I hate making assumptions, but without tearing the whole thing apart again, it's not really possible to tell.
So on that assumption, the first thing I would do is check out the ignition- check the plugs, wires, etc. are all functioning correctly - if you are missing a cylinder or two, that could cause this sort of problem.
If the spark plugs are all the same color, all of the ignition wires are attached correctly, there are no broken pieces in the dist cap, and you can get the timing light to indicate that each cylinder is firing, then I would do a compression check. Make sure that all cylinders have the same amount of compression, within about 5%.
If everything still checks out, I would pull the valvecovers and verify that all the valves are moving properly - a worn cam lobe or two can cause the engine to run roughly (what did you use for a break-in procedure?).
Just my thoughts...
-Bob Cunningham
bobc@gnttype.org
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