You are missing 4 HexNuts. I had the same problem. I found a company that sells an aftermarket add-a-trunk (besttop maybe) they have online instructions. On the instructions there is a phone number you can call. Tell them you just bought one and it was missing the parts, they will send you out like 8 of them in a couple of days.
2004 tj 4.0L I-6, Patriot Blue, Hard Top, Soft Top, 31" Firestone Destination MT's on 15" Black Eagle's, Tuffy Sub-Console and Glovebox, Add-a-Trunk, Custom Seat Covers, Drawtite Towing Package, Rampage Sidesteps, Extended Fender Flares...