That's the bad part with the MSD ignition, you have to change components to test them. Start out with some simple (and free) tests like: check for full power and ground to the MSD box, coil connections etc. remove the spark plugs label which cylinder they came from and inspect them. (may have some fouling due to the previous carb issues). Post some pics of the plugs if they don't look right. Check the cap/rotor/plug wires for signs of arcing etc. After that, I think you may need to start swapping out components, unfortunately. Is it fair to say that this issue happens at full engine temperature and/or when the base timing is less than 20 deg BTDC?