how do I go about ordering one suited to my choice of color of body, pickguard and type of neck wood?
Just to be clear here, there are several color, pickguard and pickup options. Those are what you may choose from, and no, if it's not listed you can't get it. EBMM does not do "custom" orders, period, unless you're an endorsed artist. If you work out the math for all combinations of pickguard, color and pickups, you'll find that there are currently 288 different flavors of Bongo 4 string. If you limit that to just the HH without piezo, the number of available combinations is 48.
That's based on current production options. There are still some NOS basses out there in the dealer network that sport discontinued finishes.
There isn't a great deal of stock out there especially since Guitar Center stopped buying Bongos except on a special order basis, but it does exist. All EBMM basses are built when a dealer orders one, and most dealers don't order Bongos for inventory. A black/black/maple SR4 is a safe thing to hang on the wall because it's the single most popular color/fretboard/bass combination. A Bongo... not so much.
The notable exceptions are the dealers already noted. I'm fortunate enough to have Pete DuBaldo almost in my back yard (well, an hour away) so he's my go-to guy.
If you don't find what you want in stock and decide to order, the production backlog generally runs about four months. The wait IS worth it.