I'm suprised the guys at AT haven't been on here to ask you what colors you wanted.
Seriously, everyone is always talking that Active Thunder is a Custom builder. They will make the boat however you want. If you dont want it rigged, there shouldn't be a problem. I'm sure with ThunderDan and Jassman bugging them daily with changes to their boats, it would be nice to pop something together for you that involed less decisions
Where you have the boat rigged and who does the rigging shouldn't be a problem. These big name places that were mentioned before had to start somewhere and they used to be nobodys too. From the looks of your AT last summer, you wont have any problem finishing up a boat. You might not get the same warrenty as the guys that had there boats completely done at AT but other than that it should be a go.
As fas as price is concered, I have no idea!! Start with subtracting the going rate for the items that you dont want them to put in your boat. Add some labor at the going rate and shoot them a number. Who knows, they may make you a very happy man!!
Good luck in your search!