I agree with regards to the shakedown - what's the difference between doing it before or doing it during your cruise? We did ours while we traveled along the coast and got to meet a lot of great people who helped us out along the way.

We had a similar issue with regards to backflooding. When we moved onto our boat it dropped down by about 3 inches. As a result, the vented loops for both the bilge and the exhaust dropped to waterline level and caused similar issues. The exhaust issue took a lot longer to figure out and was far more expensive, including replacing a burnt out starter motor (partial engine hydraulic lock from the backflow) and a new exhaust elbow (thought that was what might have been causing it). It's always fun to find new mounting spots when you have limited amount of space.

Anyway - lesson learned. When loading down a boat for cruising, know where vented loops for through hulls are and ensure that every one of them is above the waterline.