I'm glad you finally found the problem, it had to be a trial! My sympathies on the new engine. If possible it would be great if you could post a few photos of the new muffler arrangement.
You have me wondering if the other Super Maramu owners here have had any issues? The SM Owners Manual warns against this issue and recommends starting the engine twice a day and running for a short period to clear any water in the exhaust hose.