Phil,
You found a good site at the aluminum boat repair site that you listed. I used them a lot when I was working on mine, more for repairing rivits, etc. I didn't take out my seats but I know that the Hydrilla Gorilla site does it all the time. I think you may need to add some extra bracing. I never bought their book so I don't know the details.
A caution on the Aluminum Boat Repair board, Spike on there is very knowledgable but very conservative and is always cautioning people from adding decks or modifying thier boats. I've assured him mine is stable with the decks but he doesn't seem to beleive that it can be done. You mostly need to be aware of the weight limits on your boat.
Ken

Here's the site for Hydrilla Gorilla:
http://www.myjonboat.com/

Maybe some of the pictures can give you some ideas.