Did you discover any of these issues at the PDI, Pre Delivery Inspection? Most of these issues should have been fixed before it even pulled out of the lot. It might have been better to wait a couple days before picking it up to allow the dealer to do a thorough walk through and fix the obvious stuff. Then do a PDI yourself, and pick it up after the dealer has repaired all items on the list.
However that is all water under the bridge. All you can do now is work with the dealer and builder and make sure they do everything exactly the way you want it. But since the dealer has your money, you can only hope that they are a reputable dealer and will stand behind their work, and their product. You did say they were, so hope for the best.
Good luck, and post back as the saga unwinds. :)
