Sounds like its not the carb since you changed that out, that would have been my first guess too. I have never ran the msd stuff but there are enough that do that have had problems would focus on that.

I would see if you could install a stock points or HEI system to bypass the existing MSD to see if that helps. Ohm out your spark plug wires. Check that you are getting a full 12Volts. Maybe reset the preload on the lifters if they are adjustible. Pull you spark plugs and see if they give any clues if it only on one cylinder.

I know some people have used their timing light to find what cylinder was missing but that might not be an option if it only does this while cruising.

It sounds like you might have to much advance at cruise. Do you have vacuum advance? If so try disconnecting it and plugging it off. What is your mechanical advance?