It’s highly likely you have basically ruined the engine relays in your fusebox. These relays are designed to operate in a 12v environment, and if they are used under low voltage conditions for extended periods of time, the contacts can “chatter” and degrade the voltage that the relay can pass. If this happens, it can cause a degradation of engine performance, RPM’s dropping, or even a failure of the engines to start at all.
Fortunately, the engine relays are a standard automotive relay, and easy to find. Many owners have taken to carrying spares, just in case, because they are inexpensive, and it’s just good insurance, and one of the first things you should check if you have related problems.
I have written two related guides to this, first is a general guide describing the relays, and giving the OEM part number, and several cross-reference part numbers. This guide further describes the potential issue, so it’s recommended you read
https://www.facebook.com/groups/ChaparralVortexBoatOwners/posts/2424812577824480/
The 2nd guide is related, and discusses a relay we have found that is more tolerant to lower voltages, so seems to work better and not go bad if the battery voltage sags a bit. Additionally they are relatively inexpensive, and available on Amazon, see guide:
https://www.facebook.com/groups/ChaparralVortexBoatOwners/posts/2458079114497826/