A random mish-mash of thoughts in no particular order:
If it's truly a "miss" it is most likely an ignition issue. Assume nothing with regards to relatively new parts and inspect and TEST everything you can.
Run vehicle in the dark with the hood open, wiggle plug wires around and look for errant sparks from wires to ground, etc. If you see ANY spark, this is likely your problem...
With MSD in mind, keep in mind that your plugs are firing 3 to 4 to 5 times per ignition stroke. This accellerates the wear and tear on your plugs, wires, coil, cap, and rotor by a factor of 3, 4, or 5. Back when I ran a multiple discharge spark box on a few daily drivers I owned, I found all of those maintenance parts get replaced FREQUENTLY because they get CHEWED UP FAST. For this reason I have found little to no benefit to MSD systems, and I no longer utilize them. A properly tuned engine needs ONE spark, and any extra sparks that follow on the same stroke do absolutely nothing but accelerate wear across all of the ignition system parts that carry the energy.
Test your spark plug wires to confirm ohms per ft are within spec.
Remove and inspect your cap and rotor to ensure they are in good condition. (These REALLY take a beating from MSDs)
Confirm firing order to make sure all plug wires are properly routed.
Confirm no parallel wire runs that might cause cross-fires.
Pull every spark plug and inspect...is one of a different color than the others? There's a strong clue depending on HOW it is different. Check gap. Getting wide? Again, MSD will widen plug gap over time due to excessive erosion from multiple fires, throwing off gap spec.
Replace all the plugs just for fun. One might be defective or have a hairline crack in porcelain or similar that no testing will reveal.
What kind of coil to do you have? MSD will require a stronger than stock coil and will stress a coil much more than a single spark ignition system would.
Is it relatively easy for you to bypass the MSD box and test-drive on the straight ignition alone? If yes, try it and see what changes to exclude the box itself from being the root of the problem.
Verify your base timing. Then verify your advance timing.
Keep in mind that if it's more of a subtle/soft "miss", it could indeed be a fuel delivery issue and not ignition-related at all. Carb may be set up a bit too lean at that particular RPM/load and therefore cylinders are not getting a full charge of air/fuel to fire. If this is your problem it should show up in plug readings.
Verify your carb attaching nuts are tight and you don't have an air leak there.
That's all that comes off the very top of my head. A trouble-shooting guide in a service manual will likely provide more and better clues than I rattled off here.
Like a I said...this was just a random mish-mash in no particular order. Maybe one of the things on this list will reveal your problem. And maybe not. Hopefully you figure it out.
