Don't bother to narrow the bed unless you've got lots of extra time and money and you're pulling behind a regular (narrow) car. A roller across the back will be your first thing to do, and maybe a winch up front. Also, you'll want to go around the entire trailer with a file and file down all the places where there's a sharp edge exposed. I already knew this but after watching a buddy put a big patch on his boat at the Westwater ramp, its even more important to me now. The Triton trailers are especially bad with sharp edges...
Something you may want to put on the front of the bed is a sailboat-type rope cleat. This makes loading the boat by yourself a lot easier because you can pull the front up onto the trailer, cinch the bowline in the cleat, and then push the boat the rest of the way onto the bed (rollers are key here).
I've heard that a long, single roller across the back can warp and become useless so you should bear that in mind when you're designing it. I've got 3 rollers and its nice being able to correct the alignment as I put the boat onto the trailer.
As for decking hurting the raft, just make sure there are no nails or screws sticking up. Torx screws were what my trailer came with after you replace the decking you'll probably want to tap new holes and use some loc-tite on the new screws. Consider painting the deck - I use a white enamel and slop on a thick coat every few years.
Just remember that once you start trailering your boat, you'll never want to roll it up again.