This bit of info sounds like a bad fuel pump to me. Are you running an electric one? What type? Mounted where?
I doubt this would cause everything, but is worth repairing anyway.
I'm assuming you have a timing light. Have you tried connecting it to each plug wire to see if they all trigger the light? Try it on the coil wire too. I recently had a weak spark condition where not every wire would spark, but the engine seemed fine most of the time. Hard to start though, and wouldn't fire if the battery was even a little low. Point being, erratic spark could definitely come and go and could also cause a lot of what you're feeling.
You say the motor came from a rolled truck. I've seen accidents that you wouldn't think would hurt a motor cause all kinds of running issues. Cracked/bent cranks, oil/water which got into a particular cylinder and caused a dead hole. Have you done a compression test? I re-read and didn't see it mentioned.
Are you running stock rockers? Another thing which could cause power imbalance and the resulting shakes would be leaky valves due to excessive preload or something bent/broken or binding.
