Last summer I did what srm recommended (install ports and bolt thru). I couldn't get all the broken bolts out so I filled in the old holes with JBWeld and drilled new ones all the way thru. When I drilled the new holes, I shifted the gudgeon up one bolt diameter so that I wouldn't hit the old broken SS bolts. Since I was drilling into undamaged aluminum, I could have just threaded the new hole and screwed new bolts into the plate, but I decided to go all the way thru and install fender washers and nylock nuts inside. I filled the holes with RTV before pushing the bolts thru to keep water out.
Bill Mattson wrote a good article in On The Wire
entitled: Do-It-Yourself: Installing Deck Portshttp://www.thebeachcats.com/news/29/installing-deck-ports/
After you cut the holes for the ports, I found it easier to reach inside of the hulls and work on the insides of the transom and install the bolts, etc. before
you install the plastic ports (afterwards, the access hole is smaller)