The Mar-K tech sheet says to use 5/16"-18 x 3/4" indented hex head bolts to attach stake pocket on bed side to rear cross sill. My stake pockets have holes on both sides(front and rear). Should there be bolts on both sides or were long ones used as previously there could have been stakes there?
I'm pretty sure there were the 3/4" long bolts on front and back of the rear stake pocket to cross sill (it's been a while since I took mine apart and I don't have a snapshot of that area). There's no need for thru bolts as there should be stops in the pockets to keep a stake from dropping thru. The only thru-bolt in the rear stake pockets was for the tailgate chain, and that's offset from the hole in the bedside for a stake so the stake would miss it.
I queried Mar-K about whether they had original stake pockets (which were bent out of sheet metal and spot welded inside the stake pockets), but they said they did something differently (or left them out altogether). I bought a replacement stake pocket and it had no stop in it. Mine were all bashed completely apart, so I fabbed replacements out of 16 Ga steel.
Replacement Stake Pocket Stops