I have a 1992 502 Mag Carb., that sounds like it has a slight misfire when idling. My question is what should I check for causes. I already checked the obvious like crossed wires. I changed the plugs and replaced the plug wires. I replaced the cap, but just noticed it is not an original mercruiser. Could it be something internal. It has a standard thunderbolt IV ignition w/ MSD 6. Could the MSD have anything to do with it? Is there any way for sure to check that it is actually a mis that Im hearing?

Sure is. Its called a digital storage oscilliscope with the ability to check secondary ignition wave forms. IE, an engine analyzer scope.

The best way is by using a scope...but I guessing you don't have one laying around. You would have to run without the MSD box to test with a scope. There are other ways of testing for a misfire.

There is the old "pull one plug wire at a time and compare RPM drop" method. Don't recommend it (especially with MSD), but it sometimes works.

There are inexpensive "spark analyzers" that you can clip on one plug wire at a time. They give you information similar to what you would get from a scope. But, like a scope, you have to disconnect the MSD box during testing, and you have to know what you are looking for.

If you have replaced plugs, wires, cap and rotor with no change, a compression test might be a good idea.

Dave

Dave N is right. A miss at idle is not always ignition. A compression test is in order here. Bet you have a leaky exhaust valve.

A quick and dirty way to check is to use an inductive timing light.
Clip the pickup on each wire, and watch the flash. It usually won't flash when the plug doesn't fire. I say usually because I never tried it with MSD.
It's always worked for me on other types of ignition.

That's exactly how I do it. It won't tell you what is wrong, but it will tell you where it's wrong.