Abe--if you are moving the console to be farther from the engines, and the engine wiring harnesses are not long enough to reach between the new console and the engines, you should check with Evinrude or Johnson to see if they can supply a longer wiring harness. Although I expect an OEM wiring harness to be expensive, it may be cheaper and more easily obtained than having custom-made harnesses commissioned. If you are moving the console to be closer to the engines, you can just coil the excess engine wiring harness cable and stow it away.
I would also be leery of trying to specify and commission any custom wiring for the new installation to be constructed off-site and sent to you. You are bound to forget something. I think it wiser to find a local installer and work with him. He might have some ideas that could be useful that you haven't thought about.
If you need a new instrument panel fabricated to match the original on your Boston Whaler boat, see the recommended vendors at
http://continuouswave.com/whaler/refere ... helmPanelsI cannot offer a recommendation for "a shop" to make custom wiring harness assemblies for you, as i have never used any such service provider. But you can find many such service providers if you search for them using an internet search engine. i don't want to steer you toward any particular one of the ones I found in a search as I have no experience with any of them.