This was my solution.
3/16" Aluminum fastened with 'J' brackets and reinforced with 1" square tubing. I had previously used wood but it rotted. One advantage of the running a board or aluminum across the gunwales is that you have a place to attach rod holders, etc.
http://s1204.photobucket.com/user/tennis_pwn/media/P1010495.jpg.html?sort=3&o=1
I had originally planned on running tracks with Cannon rod holders; but, I like the way the Down East Salties work.
If you are not going to be using down riggers for all or most of your fishing, you may be able to jerry rig either a down rigger bracket or a removable plank with Scotty gunwale clamps.
http://www.scotty.com/fishing-gear-equipment/rod-holders/clamp-mount.htm