Mike:
Here is my experience, offered only for what is is worth.
In 2000 I replaced my TMD40 engines with TAMD41s. I sold the old engines privately, to a fisherman who needed them in a great hurry. That hurry meant I had no time to schedule the swap to be done by my trusted mechanic. I was on my own. I scheduled a haulout for a Sunday afternoon and had the swap done by Tuesday afternoon. I was able to get my mechanic to do the startup, just to be sure my installation was correct. The boat was out of the water, so he brought in a garden hose, opened the strainers and, one at a time, put the garden hose into the strainer and turned on the water. some overflowed into the bilge, but when the engine was started, the overflow diminished and water came out of the exhaust, just as if the boat was in the water. He spent a while checking things over, shut the engine down and moved to the second engine. The whole process for both engines took about 1/2 an hour. The engines may have been put in gear, I don't recall, but there is a bypass hose from the heat exchanger that feeds seawater to the shaft log, so that, at least, was getting wet. The outside cutless bearing would not have gotten wet. In any event, no biggie, as everything has worked properly for the next many years.
On buying the 41s, on my mechanic's advice, and because they had 1500 hours on them at the time, I pulled the injectors and sent them in for inspection and, if needed, rebuilding. I think the shop got their instructions messed up, as they missed the inspection and went right to rebuild on all 12 injectors. Also an oil analysis and changed the oil and filter on each, new fuel filters too. Otherwise, new belts, pulled and cleaned the Hxs, checked and replaced hoses as needed, and good to go.
No, I am not a mechanic. Out of necessity, I messed around lots with my cars as a kid, so lost any fear of disassembly then.