Hey Sean,
I'm strongly with those urging a call to a repudable mechanic. Even for the mechanically inclined, it takes a long while to learn a first boat, and a while for each boat thereafter.
I consider myself very mechanically inclined, but, I still keep a mechanic in speed dial (Justin @ DNA Marine, 727-934-6300) and had two on speed dial back in Cali (Chris @ S&W, 310-835-3155; Martin Ball, 310-508-9036).
Many things in a boat arent the same as even diesel truck, industrial, or farming engines. The cooling , exhaust, and transmission are all different, for example.
And, access ia very different. It is no trouble to drop an oil pan in a truck -- but try that in a boat. Ditto for smothering an exhaust to stop one.
On my first boat, it was really educational and confidence building to have Marty and Chris work on things with me around. As Marty rehabbed the two 6.354MGT mains, I did the 4.107 genset and controller.
When Marty was busy and I used Chris, he had a great ear for hearing valve timing being just a little off and I got to learn from him not just doing it by gauge, but checking it by ear.
Now I do most of my own mechanical work, but as an out of town owner, I balance my maintenance time, boating time, and budget. I try to plan to do a certain amount of work and boating myself, and hire someout for whatever is left.
Lately, the engine room has seen a lot of mechanic and less of me -- during the rare days with no rain in Florida, Ive painted the house and gunwhales and recoated the brightwork. Thats kept me out of the engine room. I am behind on fluid changes -- so Justin is doing those this week so next time I'm there, I can boat with guilt-free confidence.
When I first bought the boat it had a problem that would, by the book (workshop manual), take an efficient mechanic a full day, just for the disassembly and reassembly. Being less rehearsed, it could have taken me 2 days -- the loss total of what is, for me, a rare boating weekend. And, if I was slower, maybe two. Justin came out, told me it would be a full day, then realized a way to do it without all of the disassembly, and had it fixed in an hour. All in, including going over a tons of stuff with me and inspecting a ton of stuff, the total bill was something like $240. 2.5hrs of time.
At this late stage of the game, most mechanics are more rehearsed than me, but when it comes to 6.354s rarely have a better understanding. Justin showed me up big time (where others in Florida had disappointed). His deep understanding as an experienced generalist saw a better way. When he explained it, I was dumb-founded by the "obviousness" and simplicity. I thought I was hiring someone to turn a wrench in my stead, but, I lucked out to find an amazing tradesman and teacher.
He also showed man that attention to detail and patience can fix valve cover leaks without needing to use gasket sealer in addition to the cork gasket. He cleaned it all off and up and super carefully straightened subtle bends in the cover's lip edge. Then it mated perfectly without tightening down, so tightening it down to try to get a seal didnt itself cause slight bending. I really thought those just needed sealant, and I've seen many leaking even with it -- but I was wrong.
Back to your boat, I still dont see how a water pump causes smoke. And, I'm still concerned about the other uninspected parts of that engine. And, I'm concerned about its twin, which you described as less reliable. And, to be honest, I'm concerned the skipper/chief-engineer may still be in the on-ramp phase and beginning a long journey not yet prepared and unassisted.
