I worked for a Chaparral dealer for many years, rigged, delivered and serviced well over a hundred 26' and bigger. This was over 15 years ago so take my observations with that. Things might have changed.
I don't want to disparage Chaparral, they make a very good boat for their price point. BUT -- and this is problem with almost all boats 26' to 35' at this price point. They give them a "Yacht" class certification. But they aren't built like a yacht would be. They are built on an assembly line and the line can't stop, so this means that the boat might have been designed to have battery isolators. But when the boat gets to that station, they don't have any isolators the correct size. So they will install ACRs or VSRs that they do have on hand. Back when I worked on them, Chap outsourced the electric panels and dashes. When you forced them to build this boat with Merc power, this could have changed so many components. This means that wires and cables will be done "on the fly". So some "interesting" things can happen.
The good thing is that they now build this boat with Merc as an option. Maybe you had a hand in this?
Have you gone thru all the stuff that came with the boat? Back then they didn't come with the documentation that a higher price boat would, maybe this has changed? Things like a (I can't remember what Chap called it) build sheet, bill of materials or as built sheet. This will be a long list of every screw, nut bolt, washer and component that was used to build this boat. Also would be nice to have a wiring diagram/schematic. Understand that these might not be completely correct due the "built on a line" but would be a good starting point.
I would recommend that you call Chap and ask for these for your hull VIN and also for one of the first hulls from when they first started building this model with Merc Power. I'm guessing they should be available in a digital file.
It sounds like you are about to replace a pretty expensive battery package and charger. It would be good to check that there isn't a wiring issue that caused the battery issues. I don't know what the difference changing from Yamaha to Merc would make to the wiring, but it's possible there maybe issues due to that. Also when you install a bigger charger, make sure that the existing wiring will support the increased amperage.
You can get thru these issues. Maybe it would help to remember the quote.
"Believe me, my young friend, there is nothing—absolutely nothing—half so much worth doing as simply messing about in boats,"
This helped me and some of the techs I worked with. I still miss getting paid to mess around in boats!
