I would think that you would be ok removing and reinstalling the bolt. The only thing I see you risking is shearing off the bolt and then having to remove the entire manifold.
I think you are overthinking the situation. Water ingestion is not that common and unless someone has modified your exhaust system, I would not worry about it. I would advise not to come to a sudden stop after traveling at speed to avoid a high backwash against the transom.
I don't know that I would plan to spend 20K on a new engine and drive on a 2003 boat regardless of its condition. it will not add that to the value of the boat. I would put a re-man engine 5.7 back in it and pocket the balance. Your torque problems could be solved by changing the prop(s).
If indeed the high pressure pump is bad, there are many more remedies today than a few years ago. You can replace the entire unit with an aftermarket one for a couple hundred bucks or you can purchase just the high pressure pump and install it for cheap too. If you keep the origional unit, I...
Could be the wrong type of oil, very old oil or burnt oil from overheating. Change it regardless and I`d pull the drive for an overall inspection and service.
Are you getting any overheating alarms? Do the risers feel hot to touch? If not, the stoppage in running is probably not related to the manifold/risers.
I`d suggest you start by removing the thermostat housing and thoroughly cleaning out the internal passages. There are a few that can be hard to find if you do not know where to look.
For what little they cost, I would probably try one of those $200 aftermarket pump assemblies to see if the whine persists. Worst case scenario is now you have a back up pump.
I purchased on of Stumpy`s stands after using a home made for years. The Stumpy`s is much nicer in that you can adjust the height of the stand much easier. If you plan on using it often. I suggest Stumpy`s.
