Yes, I had pulled the engine last year to replace the coupler and engine mounts. Don't think this is related but there was some "forensic" information revealed when the engine came out that may be related. Short story, I bought the boat from the original owner in January 2010. Older gentleman had the boat in dry storage for 10 years. Before that it was rack stored. Less that 100 hours but the first year issues like fuel pump, frozen starter, carb rebuild, etc were expected. Ran the boat for 3 years with no real issues. Two years ago when we replaced bellows, gimbal bearing, etc, we found water had entered into the top of the outdrive and damaged the gears and yoke so rebuilt that (gear oil showed no evidence of water and the O/D was performing OK but decided to fix what would fail in the future). When we pulled the engine last year to replace the coupler we found a very definite rust line about 1/3 of the flywheel so I replaced that. We figure that while the boat was rack stored no one pulled the plug so rain water likely gathered in the engine compartment to at least 8" deep and sat there for sometime resulting in all these issues. Some things you just can't see on a normal inspection.
Plan now is to pull the boat after the holidays, yank the engine and O/D then roll the boat into the garage. Sometime after I heal from the surgery I'll go about the task of cutting out the transom from the interior, clean out the rot and rebuild it with 3 sheets of marine plywood, epoxy and fiberglass. Some fun, eh?