More thoughts on my wild guesstimates.
Here's a write up on repowering a 34 ft Mainship. This link is to page 6 of 6, the costs. Runaway - Repower of a 34 ft Mainship
project costs. Unfortunately there is no date on the write up so adjusting for inflation is not possible. His costs of $19,804 are doing most of the labor himself. I can give you one example of the difference between DIY and hiring it done. He has the cost of a new shaft and coupling at $948. So two shafts would be $1,896. I have an estimate for new shafts for a Californian 42 at $3,000 to $3,500.
If you are up to DIY repower start your thinking at $39,600. If not DIY then a rule of thumb that I use for first pass on big project rough estimates when I hire the work done is 2 X whatever "it" costs sitting on a palette next to the boat.
Reading the questions you've asked in other threads and the fact you don't live near the boat I'm thinking DIY is not an option for you.
Taking the small amount of labor out of his costs I get $18,964 for one engine. $37,928 for two engines. $75,856 for the job hired out. I always add 25% for growth and it usually comes out to more than that. Now the guesstimate stands at $94,820.
Things to think about other than costs.
- Length of engine, will the new fit.
- Height of engine from mounts to top most part, will the new fit.
- Depth of engine from mounts to bottom of oil pan, will the new fit.
- Actual HP required to use the boat the way you want to.
- How will the old be removed and new installed? Do you have good enough access through doors and hatches or will the boat have to be cut open to do the work?
- Are your fuel tanks outboard of your engines? If so time to evaluate them and deal with that issue while the engines are out.
That's just the 'get started' thinking about it list. I suggest a membership at boatdiesel.com and start reading.
With ford/fiat engines and the age of the engines and boat you are not likely to find a quick swap like repowering a late model vehicle.
Sometimes the best option is to sell it for less than you paid for it, take your lumps and walk away. You've asked about control cable problems, water tank leaks, electrical problems. What else is lurking on the boat that might be more expensive than those relatively minor items? What will the boat be worth after a repower?