Hey Greg-
You know that every Alembic is slightly different. If you haven't already owned and played a bass, you don't know if it will work for you. I wouldn't sell the Series I until you have had the Series II for at least six months. At that point, you'll know which bass speaks to you better if one even does. You may find you use both, or that one never leaves the case.
Even if you're still thinking about ordering a new II, I am a big fan of buying used for research. If you buy the bass you're looking at, it will either confirm or alter your perception on what you'd want out of a custom. You might find that medium scale doesn't work, or that it is perfect. You might find that you wish the string spacing were a little wider or a little tighter and be able to specify that to perfection. You might find that the upgrades in the Series II don't do anything for you over the Series I that you already own. After your research period is done with the used bass, you can probably sell it for most of what you paid if you don't love it. Even if you eat $300-500 on the deal, it's good insurance against a possible $5000 mistake on a custom order. $5000 being an estimate of what you might lose if you have to resell a custom Series II that doesn't work for you.
As far as value of your Series I goes, you should be able to make an immediate sale at $3500, a reasonably quick sale at $4000, and patience might get you as much as $5000 depending upon the appearance and features of the instrument. If there's someone out there thinking about ordering a new bass like the one you're selling, then it will be very appetizing at half the cost of a new one. It's an odd market right now and the bottom could drop with this economy at any time.