I had a similar problem years ago on my 1990 Chevy dually with TBI Bad misfire under load, and slightly at idle. Thought is was the timing chain, nope. It turned out to be the upper bearing in the distributor went bad and was causing erratic spark. The only way i found it was I had the cap off and watched the cap turn. I noticed that it wasn't a complete circle. grabbed the rotor and could feel the rotor move back and forth. It wasn't enough to cause the rotor tip to run into the tower but it was enough to give the pickup a bad signal.

another cheep way to diagnose the problem to one cylinder would be to take a temp reading at the exhaust manifold with an IR temp gun from Harbor Freight. comparing one side to another might tell you something.

I wanted to follow up on this post as I never had a chance to do any in water testing as the weather changed quickly last fall. Over the winter I checked everything I could possibly think of. Cylinder leak down test, Pressure tested the headers, etc., etc. Looked for hours and never could find anything wrong.

Today I finally got to put the boat back in the water for a test to see how it was going to run. Ran perfect all day.

So to answer my original question is, yes a plugged exhaust will cause an engine to miss fire.

Thanks to all who responded as I appreciate all the input.