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Wow. Sorry to hear you are going though that. All that puts tuning up a 1990 Yamaha 225 and replacing a deck in an old 1979 Revenge into perspective.

I have seen boats that are for wahtever reason, simply "cursed". If I were in your shoes, I'd have a meeting with Whaler's local rep and layout everything on the table. I would not have any confidence in it either so if they do not put you in a boat that's not a lemon (or at least swap out the engines), get it fixed and sell it. Cut your losses. Then look into a different boat manufacturer that's not tied at the hip with Mercury.