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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