Re: wire turned black
Well, this particular wire is a wire that you really want to do its job well. Many others are, too.
It would be worthwhile to check the wiring on nav lights, engine controls and instruments, and signalling devices to verify the proper wire was used. Secondary circuits, like stereo, livewell, and the like could wait. Marine wire is the right way to go, and for the very reason you've witnessed. If Bayliner used something else, well...
It's always possible that a previous owner replaced or added some wiring with whatever was kicking around the shop, or the auto parts store. And most anything will work for a season. Trouble comes when you're a few seasons down the road from the now-forgotten quick repair, and a bilge pump suddenly becomes "mission-critical".
Solder is good if you're good at soldering. Marine shrink tubing (with internal adhesive) is good, too.