Here's my .02 cents. This is how I would do it if it were my boat. Not to say that my ways are right.
Question 1: 6061 has rounded corners and is generally used for structural applications where strength is important.
6063 has sharp corners and is generally used where surface finish is more important than strength. Brine has an exceptional build where he uses a lot of 6061 angle for deck supports, but even he admits that this was probably overkill. I think 6063 would have been plenty strong and easier to work with.
Here is his build link for some ideas: https://www.tinboats.net/forum/viewtopic.php?f=21&t=6551
Here is the link to an online metal supply store. I'm not suggesting you buy from them, as it would be way cheaper to buy your aluminum from a local retailer. There is, however, a ton of useful knowledge contained on this site so you can educate yourself on what to buy. https://www.google.com/url?sa=t&rct=j&q=aluminum%20plate&source=web&cd=1&cad=rja&sqi=2&ved=0CEkQFjAA&url=https%3A%2F%2Fwww.onlinemetals.com%2Fmerchant.cfm%3Fid%3D239%26step%3D2&ei=_lFjUcGBPYqs8ASd2IHoBg&usg=AFQjCNEsuuPiOG-1N7xFz4PynKooDKEHPA
Question 2: I would only weld in my flooring if I had access to my own equipment, and possessed the skill to weld aluminum properly. Paying someone else to weld up your boat will add up real quick. Also, if you weld something slightly off, it's a pain to cut and grind it off. Riveting is very popular because it can be made strong, done fairly quickly and doesn't require a ton of skill to master. If you make a mistake with the rivet gun, you can drill out the rivets and start over. Just like with anything else...measure twice, cut once. I would only use screws sparingly, and in places I access frequently. If you screw something together under the deck, who's to say that your screws aren't backing out on you in that heavy chop? If it is an area that you access often, you will be able to identify a loose, or backed out screw and tighten it. Make sure to use good quality SS hardware if you screw anything together. You'll thank yourself later.
Question 3: Check out Steelflex by Fasco. It is one of the most popular paints/epoxies on the market for painting an aluminum hull. Whatever paint you decide to go with remember, 90% of a quality finish lies in the prep work. Only 10% actually involves painting. Here is a link to another similar thread on TinBoats.
https://www.google.com/url?sa=t&rct=j&q=steelflex&source=web&cd=1&ved=0CC8QFjAA&url=https%3A%2F%2Fwww.tinboats.net%2Fforum%2Fviewtopic.php%3Ff%3D3%26t%3D8804&ei=9fNdUbbfDo7M9gTW8IDoDw&usg=AFQjCNF_jbJ-43-6fhwt13ludenMObzKRA&bvm=bv.44770516,d.eWU