-- Last Updated: Nov-13-12 7:36 PM EST --
If you get D-rings with the strapping sewed onto a patch of vinyl, you can bond that to the inside of the hull really well using "Vinybond" (the stuff looks and smells like the solvent that's used for bonding inner-tube patches).
For building a float-bag cage, the "standard" method is to drill holes through the hull just below the gunwale, about four inches apart, and use them to lace a crossing network of cord over the top of the bag. You can install screw-in eyelets under the gunwale to do the same thing, but to some extent that weakens the gunwales against lateral stress (like what happens when running sideways against a rock or tree), while drilling the hull has virtually no negative effect on strength. In addition, you need one or two straps over the bag running from the tip of the hull and down to the floor at the "fat end" of each bag, to keep the bag from sliding out from under the cage of cords. I just use a fat rope instead of a strap. You'll need a well-anchored D-ring (or two if you use two straps) mounted on the floor. A hole drilled sideways through the tip of the hull or perhaps a vertical hole through the deck plate can anchor the other end of this strap or straps (or ropes). If you look at the photos linked below, that little bit of white rope that's visible on the outside of the hull at the very tip of the bow and stern is the anchor point for the strap (rope) that runs the length of each float bag.
(Click on "actions" > "all sizes" > "original size" for a larger image)
Threading skinny cord through holes along the edges of the hull is no big deal if the cage will always be in place, but if you plan to remove it now and then you'll get pretty sick of the job, and it may even prevent you from making the switch to caged or uncaged, just because it's no fun. Here's a trick I use to cut lacing/unlacing time to a tiny fraction of what it otherwise would be:
Thwarts can be varnished or oiled. Chances are the boat came from the factory with an oil finish or a "barely even there" coating of varnish. Some people like to varnish the end grain of each thwart, and periodically oil the the surfaces that are always accessible. The pluses and minuses of oil versus varnish can be talked about if you are interested. Everyone has their favorite method, which usually partially depends on a few factors such as where the boat is used and whether it is stored inside or outside.