The timing problem could be as simple as the outer ring on the damper has slipped and the timing mark is not at TDC, so agree that needs to be checked.
It is also possible that the two wires going to the distributor are paired incorrectly. Try swapping those two and see if the motor runs better.
As part of the HEI upgrade did you remove the lean burn distributor and install an electronic Mopar slant six distributor with a vacuum advance can? The lean burn distributor has locked ignition timing.
Lastly, if the carb on the motor has wires going to it from the OE Lean Burn set up. That carb will never work right with the Lean Burn removed. You need a non Lean Burn carb.