Wash your hands and clean your boots, Scoots

I'm going with Mark on the stain right after plane plan (I'm a freekin' poet today...!) The planed wood will take the stain nicely, better than sanded wood.
But let the stain sit for longer than just a few days - give it at least a week. Longer if it's oil. You'll find that prints will wipe off better without taking all the stain with it.

As for rotting from the inside out...unless you're wrapping the timbers with cellophane, I don't think that it's an issue. Hell, my mother has a gnarly old tree trunk coated with about an inch of varnish (70's hippy wanna-be art) and it's not rotted yet, unfortunately....