I second what Hollis suggested. (He would know, scoring a half-off-new deal on a superb custom DaSilva not too long ago). If you are open to someone else's custom choices, and a patient buggah, fantastic deals can be had. I've bought several custom, one-of-a-kind ukes for 30%-50% off the price of new, on eBay and UU Marketplace, over the years, not only saving money up front, but i resold without a significant loss (the first guy took the skinning..lol).
Keep in mind, if you are the original ordering buyer, that, while there are tons of people lusting for a Kamaka, KoAloha, etc., that sound indistinguishable when blindfolded from a custom, there exists far fewer that have heard of, or will want to pay a premium for, a custom by many of the custom names that often come-and-go. Just a few years back, the ultimate customs--top shelf all the way, everyone drooling for them--included Glyph and King and Kawika. I'll bet the vast majority of the people on UU now never even heard of those amazing luthiers; their willingness to pony up thousands for one of these luthiers' ukes: zilch. (Those ever-diminishing numbers who recognize their work as legendary would, though). There are many customs (DaSilva, Barron River recently) that have languished through many price reductions on UU Marketplace before finally selling.
Of course, if one keeps the uke forever, it's a nonissue. I'll add that, in my experience of buying and selling many, many ukes, one thousand dollars is a magic price point. Easier to sell ukuleles below that four-digit number than above it; this is particularly true with the softening enthusiasm for the instrument recently (I would know; I have four ukes eating dirt on eBay right now...lol).
Like anything custom, it's yours if you buy a new custom uke. Too quiet? You think it's overbuilt? You find the finish too heavy, or the tuners unsmooth? Well, it's yours regardless. No play before buy, generally no returns (especially if you order your nickname in abalone inlay down the fretboard...lol).
Those are just things to keep in mind. The best custom I've personally ever owned? Agree with mountain goat: my PoHaku. Amazing intonation, workmanship, and tone. It was superb in every way. And, like a ninny, I sold it--at a loss--to afford some other custom that I've long since forgotten.
It is fun to order a custom, though. Everyone should try it once.
Once.