For the big cross bolt that tightens the top and bottom together? That's a 3/8" allen socket. I bought one off Amazon just for it, and it stays in the box with it for when I need it. Also, you're supposed to torque it to 35 ft. lbs. to hold a barrel in place and keep it from slipping. Be sure to use the supplied non-adhesive drywall tape around your barrel shanks. It works like rosin, but without the mess, and it will protect your finish.
Sunex 3/8" Allen Socket
As for the ARCA base missing parts, I'd just call SAC direct and ask them to send you some. They have good CS.