Unless you are absolutely fanatical about duplicating the factory build it kinda doesn't matter. You could use all short bolts.
The only reason they mixed and matched in the factory was to give easy access around the fuel tank or crossmember clamshell brackets to the guy in the pit tightening them down. He was doing 8 bed bolts every 45 seconds (60 jobs per hour) - plus hanging the spare tire - so he had to be quick.
I don't recall for sure but I imagine there could have been some variation between long vs short, 2wd vs 4wd, half/three quarter/one ton, single vs dual tank, and exhaust routing too, based on the above.
On my '87 short box I believe both LH and RH in the #2 location were long.
K
