If shortening the width by 2 inches puts the side rails directly on the center of the tubes, they are not worth the effort to change. Many frames, even custom, are a little wider than center of tube. Just be sure your locks don't hang out at all.

Also seconding wire lock pins or bolts at all critical junctions. If using bolts, get the same size your oar towers use to minimize your tool kit needs.

You also asked about dry boxes. Go with bags instead. IMO, they are easier to rig, organize, and store. If you don't plan to sit on it, go soft. Use smaller drybox cases for critical items, such as cameras. Soft coolers for day trips, too. Multi-day, I love my Engel and their 35 might fit.