With both Border Reivers and It's Alive! I had a spreadsheet which tracked what the status of each numbered copy is: ordered, sold, shipped, etc. I've numbered the copies in the hope that it will make the games more appealing to collectors, though I don't know whether this is actually true.
Anyway, with Border Reivers I had only one hundred copies, and only ten pre-orders before the game was released at last year's The Cast Are Dice. Most of those were from friends and family who I knew would come through. As the game progressed if people enquired then I would offer to hold a numbered copy for them, e.g. I'll put number 37 aside for you. In some cases it took a couple of months for them to pay for the game, but that was no problem. However, in one case the customer hadn't realised just how shockingly bad the UK/US exchange rate was, and when he did he couldn't afford it. I was now left with a copy with a lower number that I had to allocate to someone else. No biggie.
It's Alive! is on a different scale however. I'm making three hundred copies, and I had fifty pre-orders before the game was released. Again I offered people numbered copies. This has been more troublesome. I've had difficulty contacting some of the customers to let them know their copies are ready, some people take longer to pay than others, and a few people have pulled out. I have to sort through the rulebooks (where the numbers are recorded) to find the right one when I make a sale, and I've a few low numbered copies that I'm holding for customers who might not come back.
There's a couple of things I don't like about this. Getting a low numbered copy is supposed to be the reward for ordering the game early, not the reward for being the first person to buy a copy after someone who ordered early pulls out. Also, even though the rulebooks are in numerical order and grouped in sensibly sized groups with a post-it note describing their range, it take time to find the right one. Not a long time, but probably getting on for a minute. And I've got to do this three hundred times. That's getting on for five hours hunting for the rulebook I promised someone. Life's too short. And I'm too busy.
For my next game I think I'll change the plan somewhat. As people pre-order the game they'll be added to a waiting list. When the games are ready I'll contact people on the waiting list in the order they contacted me, so early adopters have the chance to get low numbered copies. However, what I'll do is assign copies in the order that people pay me. That way the rulebook I'm looking for will always be the top one.