The Custom Shop just took a pretty noticable price increase recently. You can run through the spec sheet exercise like dreads suggested and see what you get quoted. Hopefully a dealer would cut you some break but it still may shock you on what the actual price is, depending on what you want on your guitar.
I hang out some on the Charvel Jackson Forum and there are a lot of PO'd guys there over the new prices and the very long wait times with the Custom Shop. You might also consider some other custom builders such as Don Grosh, Suhr, etc. and see if they can build you a guitar that you want for a better price and with a shorter wait.