If the MSD box is bypassed, what system is running the engine?
How do you know its age? and can you give us more details on the system? (Like a model number, or some way to identify it)
Boat's generally run by engine hours, not odometers. Most boats don't have odometers (I've not seen one, but they may exist)...
Boat manufacturers don't make engines, they ONLY make boats. They ALL buy engines in from marine engine suppliers, like Mercruiser, Volvo, etc. Being not the original engine is NEVER the problem.
There is a correct procedure for adjusting idle. I suggest you get a hold of Merc service manual #9 and have a good read. In the meantime, the idle is 650-700rpm, in forward gear, in the water, unrestrained (ie, not tied to a jetty!).
The next thing you should be doing is opening the throttle fully and removing the flame arrester (looks like an air filter) and looking at the throttle plates (you'll have to push the secondary air flaps open with your finger) and making sure the throttle plates ARE fully open. And do it with the engine NOT running. (Yes, I have seen people try to do it with the engine screaming its box off.
)
Chris......