Ive never had a custom boat built as well but have had a few boats over the years. One huge thing I like is a 12 volt plug in for spotlights, etc. Also a drain on each side of the rear of the boat vs just one side, and an over-sized drain never hurts either(ya get a lot of crap in the bottom of the boat getting in out of it during the season).
A quality electrical panel is also a must have imo, the last thing you want to deal with is some cobble job of corrosion nightmare(learned this one the hard way)
Handles on the rear of the boat and one on the front(for strapping/trailering purposes and pulling), also anchor ties on both side of the boat vs one like I have now.
Ice breaker are also nice if your more north where you get ice, I also like trim tabs, have buddies whose boats would porpoise with out them.
If your going with a narrower boat, Spud pole kit is nice to have.
If you run heavy mud or get stuck a lot, a welded bracket to support a winch is a damned nice thing to have, along with a winch obviously.
These are by no means essentials, but def something's to consider.
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