I don't know how much I can help, seems like the best answer is to go through the manual again and see if any of the pieces are duplicates or extras, or if you missed them.
A look at the manual shows that pieces bottom row second from left are used to hold the bearings to the sled. There are 4 of them.
The rod at the top looks like it could be any of the rods. They are in pairs, two for x, two for y, and two for z.
Might just need to go back through slowly and see if you find them.
Good Luck
