Boat started and ran fine for about 30 min. Then began too run a little rough, and did not want to idle. after a while it cleared-up and was fine for the whole day, starting and stopping several times. Next time out the boat started fine and ran for about 1 hr.stopped for lunch. When attempting to start the boat it did not start right up as usual. Pump the throttle and it would kick-back and backfire, almost as if it had jumped time. long story short....... I swapped out the MSD system and re-installed the old Merc.thunderbolt system and the boat runs fine.
Has anyone else experienced a similar problem with MSD?
What was the cause of the failure?

Do a search here in the Tech section for MSD, you'll find your answer.
They dont seem to be the most reliable in marine applications.

Did you use a 6m blue Marine Box or a Red Automotive box?

Could be a defective magnetic pickup inside the distributor. I had it happen to 2 of them. Summit stocks them.
Due

Could be the pickup as Due said.

Also check all your connections dilligently, hot and ground. MSD's are notorious for screwing up with "any" loose or marginal connection whatsoever. Being your problem seemed intermittant, I'd sure double check all that.

Thanks for the advice guys!