I'm surprised no one else has confirmed my comments about ordering. When I bought my TDI(s) (one in Dec 98, the other in Nov 99) "ordering" was a frequently discussed topic here--perhaps because it was even harder to get a TDI back then. I'm absolutely certain that at that point no one could order any VW vehicle. You got to choose from what was being made and if your dealer was resourceful and lucky, one to your specification could be found, but definitely not made specially for you. I've never heard that this system changed, and really, I doubt that it did. Many dealers accept "orders" but don't really tell you that you the only thing you've "ordered" was to have the dealer search as far and wide as possible to find the VW that you've "ordered", and if not found, to wait and keep looking as new lists of VW's in production come in. Lazy dealers often seem to sit waiting for your "specifications" to randomly come in--and if you wait for that, it could be a long, long time. The general recommendation in past years was to call far and wide (as far and wide as you'd be willing to drive to pick up your beetle). If you expand your search with phone calls to dealers in your state and surrounding states, I'd bet you could find something pretty close to what you want without waiting. Of course, there's no guarantee as to what kind of deal you'll get. BTW, $1000 deposit seems more than "the going rate".
I'm getting kind of long winded here, but let me summarize what I did to get the cars I wanted. I was living in Portland, OR. In Dec 98, I called all the dealers in OR, (about 6), then ID, WA, NV. No one had a beetle TDI, or if they did, they were asking more than MSRP, which I wouldn't pay. I then started calling some of the CA dealers, and lo and behold--a San Francisco dealer had what I wanted for $500 under MSRP, which offset the $600 to ship it by covered truck. I gave him a $500 credit card deposit to hold the car while all the paperwork was done (all by mail). The second time I got a car in Nov 99 (I just had to have one with the newly available leather and sunroof--call me crazy) I did the same thing. No one in Portland had one. I expanded to Seattle and found one exactly as I wanted. Put a $500 deposit on credit card over the phone, drove up there and bought it and drove it home. You can wait if you like, but I'm not that patient. Good luck! The wait is worth it.