If you really like the boat and have no intention of ever getting rid of it, I would go to Jeff's or somewhere else and look for a lightly used 4-Stroke.
http://jeffsoutboards.com/for-sale.aspx
You get out on the ocean and intercoastal waters you will see an awful lot of 15-20 year old boats with brand new engines. They put enough hours on them to where they go through 2-4 motors over the life of the boat. We are kind of strange up here in that we have a tough time convincing ourselves to repower an older boat.
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I forgot to add a question about your overall thought(s) on the rest of the motor. Does it have a ton of hours on it to where a lower unit or charging system are not only next, but soon? You would hate to sink $2-4k (I have no actual idea what it would cost to rebuild) into a new powerhead only to then have the motor nickel and dime you with $1k repairs shortly thereafter.
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p.s.s. I would seriously consider upgrading to that 2014 4-S Yamaha with 115 horses under the hood. It would seem like a whole new boat if you put something like that on it!
