Replacing the upper drive in a Mac Mini Server:
1) disconnect the heat sensor from the motherboard as shown for the lower drive in step 13. This is the 2-wire socket adjacent to the fan socket disconnected in step 5
2) remove motherboard (see the iFixit guide)
3) remove power supply (see the iFixit guide)
4) remove T6 screw holding the plastic retaining bracket to the aluminum shell. With the screw removed, slide the plastic bracket out the back. The lower drive will come along with the bracket
5) remove the 4 T8 retaining screws in the sides of the drive unit.
6) remove the black tape and carefully remove the heat sensor unit just like steps 18-21
7) remove the SATA connecter
8) if you're installing a thinner profile drive, like an SSD, you don't need to use a spacer because the 4 T8 retaining screws "suspend" the drive in the right position relative to the lower drive.
9) reassemble everything in reverse order.
If you're slow and careful, this isn't any harder than the lower drive procedure.