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replace the wire if you want, i would.....but they aint bad. its the connections. junction box, switch, connections. trust me. wire is fine, its the stops it makes along the way that just dont work. but, i would replace it all. because thats how i am.
I have seen the wires run into plastic tubing neatly clipped to the port side gunnel, then run up to the bow light on some 13' models (not factory of course), it didn't look so bad, I think it was done so the lights worked, and the boat got in the water that season w/ working lights. The foam core is in the hull, so running through it is pretty much out of the question.
If you are replacing the rubber, I think you mean that you are going to put on a new rub rail? Is that correct? If so, you will find rewiring your bow light to be a very easy and intuitive thing to do. Your new wiring will run enclosed in the new rail. You'll see.
Don't be afraid to warm that replacement rail up a bit either. They are pretty stiff. A heat gun works fine. Have a rubber mallet handy as well. You should not need it much, but there will be a few spots that need a little persuasion!
Good Luck,
Grady