Whatever you do, make sure you get at least one Ebony neck laminate. It's the single biggest thing you can do to awesome-fy your tone.
If you're planning on getting Anniversary electronics and later upgrading to Series, make certain you specify that you want your bass to include the prep for future Series upgrade option.
I recommend getting continuous wood plates as an option -they look great and take off weight. However, if you do get these and/or get LEDs, you need to think about coordinating the plan with the Series prep.
The Series prep includes Alembic drilling out (in advance) the cavities you'll need for your eventual upgrade to Series, and applying the silver shielding paint, and adding the dummy pickup and the 5pin jack.
It's recommended that you make it clear that you want to be able to upgrade to Series in the future as this requires a slightly thicker body to accommodate the electronics.
If you opt for a Rogue body, you'll also likely need the Pregnant Rogue body variant -again to accommodate the future Series electronic... so again it would be important to make this clean before and/or when you order.
I give a hearty recommendation to the Balance K body shape.
But make sure you get an Ebony neck laminate; even one will do the trick. If you haven't heard about it, ask around, and everyone who has one will back me up on this.
One last thing: if you get LEDs, you might be able to have them and your power run through the 5pin jack, in which case you could avoid a battery cavity for LEDs and save a little money by not having that and not needing a continuous wood plate for the cavity (assuming you get that option). But this would mean you couldn't use them when playing wireless (if you do or want to be able to).
Just a few things to consider as you order your custom.
Oh, Coco Bolo looks and sounds great, too!
What scale length are you getting? Shorter is better unless you're getting a B string, in which case you shouldn't go shorter than a 33 or 32 inch scale.