I say keep it. If it is being completely gone thru, and you are not after high horsepower, closer to stock, you should be able to get some guarantee on it!!
We had Bill Scotten building our engines before we ever bought our 1st CP. Engines were always warrentied until we headed up in HP(over 650) Never had a problem with any of the motors, just wanted to go for more.
As to cost, this is the 3rd motor in our boat, one modified once. After stepping up each time, and the last being the twin turbo, we could have bought a much larger, more expensive ride. We even have our last motor for a 'spare'! Just enjoy what we have!! Moving up? That's a decision only you and your family can make.....But you have a beautiful boat!!!!