Re: 3.0 under water
OK, you really have three options here and they are independent of each other 1) Assume everything is working correctly and in good shape because the repair shop said it was 2) Begin your own investigation 3) Take it back to the repair shop and inform them you still have the water problem, but it's not from rain like you originally thought.
Number 1 and a good tow line will get you out on the water, i.e. it's out, because you know you're stil getting water in your engine. If you told the tech that your engine flooded due to rain, they cleaned it out for you and probably did not go into too much detailed troubleshooting for the source of the water as you told them where it came from. If you had told them you were getting water in your engine from an unknown source your results (and bill) would probably have been different.
Number 2 is what the people on this board can help you with. Somewhere in the archives there is a diagnostic list for water ingestion. You need to go through it step by step until you find your problem. If you don't want to spend the time diagnosing it and working on it, then
Number 3...
I suggest number 2. The faster you de-mystify marine engines the more money you will save and the more confident you will be going out.
The muffs you saw do in fact supply water to the engine. A small leak may not show up in 5 minutes of running on the muffs. Find the dianostic, or maybe someone will post a link to it.