Couple of observations...
1. I see 8 nuts, 2 bolts, and 2 studs that came out with the nuts. That equals 12. There should be 13, so I'm thinking you missed one.
2. The conical nuts/washers are installed incorrectly on the two studs shown. The cone side of the nut should fit into the cupped side of the thick washer.
3. To answer your question about the ends of the bolts... These bolts/studs go into the water jacket, so the ends have corroded off due to the coolant exposure. When you reassemble, use thread sealant on the bolts and studs. Not all go into the water jacket, but many of them do.