#1 - The four large holes were for the CJ3A spare tire mount. Since the military moved the spare mount to the tailgate these holes were plugged with 2 bolts and two left open
#2 - There are only four holes in the tub rear bed. One for the gas tank hold down, one for the driver's seat rt rear leg and two at the crossmember mount pads.
#3 - There are 4 pairs of holes for footman loops. Looks like you overlooked the filled inboard rear footman loop's forward hole.
#4 - OK
#5 - OK
#6 - You have 5 unmarked holes that do not belong there. You have two pair of 2 holes unmarked that do belong there.

Orange X marked holes do not belong. The two pair of holes circled in Orange do belong. They are for the seat back retainer hooks.