Shield footprints - They should line up - I started with the duemilanove footprint and never touched the shield headers - only enlarged the board around them. The perspective might look off due to the board being longer & wider.
Website - Yeah, Skyjumper might be a little ahead of the game - or I am in posting that. But it does look sharp!
Selling - I think I'd be up for selling bare boards and/or kits from a pick list - you get all this with every kit (a,b,c), pick from the following: 1 of w or x, 1 of y or z. I don't know about completed boards, I don't have time to line up an assembly house, nor time to assemble them myself. Maybe just have the FTDI chip soldered, folks can hand solder the rest depending on what they want to implement. I think build at least a couple and make sure every thing works as expected.
Got the labeling cleaned up last night, will create gerbers tonight & review, then I think its time to place an order and buy some parts!