JimJay
HOw fast do you run the boat NOW?
Do you have any plans to plane the boat ?
If you don't plane the boat and do not intend to you don't need the aftercooler function. A 36 ft boat will operate easily at about 7.5 knots burning about 4-5 GPH . That will produce about 60-70 HP total from your engines and I'm being generous. Each engine will use about half the fuel and produce about 1/2 of the total HP which means that the turbo and aftercooler are simply excess weight aboard.
The only time the turbo and aftercooler would likely come into play is if you pushed up to 10 knots or beyond. Beyond definitely, 11K +, would bring the turbo and aftercooler into play.
If you want/need to be able to run substantially faster than hull speed then the turbo/aftercooler would be needed.
If you would be happy keeping the speed to under 8K then the engines would be just fine.
Bypassing would give you time to search around for a replacement or repair, maybe even a worki around with a different but suitable unit.
Companies like Trans Atlantic Diesel, Gold Coast Diesel, who repower boats may come up with units if you contact them. THere are other sources.
The link to Bowman may also be helpfull for repair.
Do a guest appearance on Boatdiesel. com and peruse their advertising section as that may help with other sources. THey have private ads and commercial ads. Ebay?
JMO