When i replaced all my bunks i used a router to take about 3/4" of an inch out of the top of the board and then used bolts and lock nuts to through bolt all the boards down and fills in the excess area on top with silicone to keep water from rotting out the wood. Seems to work pretty good so far. I was in the same boat as you though with the lag bolts rusted and basically falling out of the bunks.