Hi Kawartha92. Cool new toy you've got there. The beauty of aluminum boats is that you can do pretty much anything you want to them with pretty basic tools and techniques. There are really only a few rules to remember when it comes to tinnies; 1.) NEVER use pressure treated wood as it will cause pitting in any aluminum it comes in contact with. Instead, use high quality, exterior grade plywood and seal it. You can use spreadable 2-part epoxy, Spar Urethane, or even several coats of good exterior grade paint such as Rustoleum Professional Oil Based Enamel. 2.) To mount it to the hull you'll want to use aluminum rivets and/or stainless steel hardware dipped in 3M 5200. 3.) You can do any framing within the hull using 2"x2" non-pt lumber and/or aluminum angle and tubing. That's really about it. The rest is simply a matter of time, money and creativity.
As for the current leaks, 5200 isn't the best ting to use. Instead you'll want to either rebuck the current rivets, drill them out and replace them, or simply paint the interior seams of the boat with a product such as Gluv-it. You never want to repair anything below from the outside of the hull, always from the inside out (i.e. seal interior seams rather than exterior). With the exception of epoxy products, which you can order online or buy at boat shops like West Marine, you can get everything you need at any Lowes/HD.
With regards to your layout, that will mostly depend on what type of fishing/boating you do. I have an old '59 vintage, aluminum runabout that I converted to a flats skiff, while other folks have converted skiffs into bass boats and cruisers. It mostly just depends on what you like best. The first thing to decide on is if you're going to use a helm (steering wheel with controls), or use a tiller to run the motor. If you use a tiller, I would suggest a tiller extender and grab bar, both of which you can make. If you're going with a helm, I would suggest a small center console, but others like a side console arrangement.
