There are many rod builders out there that can build you a rod. Some are members of this forum that build for fun and for their own clients, some are sponsors, and some will pop up on a Google search. To me it is kind of like finding a good, honest, and reputable mechanic. Lots of guys do it but their style and craftsmanship may not be what you are looking for either. The builder you choose should be able to execute your build idea and help with questions and fitment issues among parts you choose.
Also keep in mind the hidden costs that most builders won't always tell you up front.
-Labor cost to build the rod - This may vary a bit depending upon who you go with - I would figure a good $50 - 100 here
-Shipping the rod - They aren't like a larger retailer who will ship a rod for free - expect $25-35 here
-Shipping the rod components - All places that I am aware of will hit you with a $10 charge for all rod blanks shipped
- MSC supplies - Rod epoxy, finishing products, and other supplies that they may need to use
-All of your components - Blank, guides, reel seat, cork/foam grips, but caps, foregrip parts, thread wrap, etc.
Pick a custom rod if you have the funds and the want to have something unique and built in specific way with certain components. Keep in mind that more bling and trim pieces you add the more the cost goes up.
Choose a shelf rod if you want a lower cost, ability to recoup more of your cost should you sell it and overall better warranty support. If your custom rod fails it may only cover the blank. You still need to worry about having the rod re-done with what components could be salvaged from your failed rod.
Customs and factory rods appeal to folks for different reasons. I would look into both before pulling the trigger either way...