I just installed a Samsung SSD in a brand new MacMini Corei7. Surprise! It had the HDD in the lower (actually the upper) bay. And then you have to completely remove the logic board to get to the two screws on the side of the HDD. Just follow the steps for 'installing a second harddisk'.
Interesting detail: the two holes in the logic board where you have to put the 'logic board removal tool' are aligned with two plastic rings glued to the aluminum frame, so you actually use the tool as a lever to edge out the logic board.
One question remains: is the SATA cable for the lower position identical to that of the upper position?
In the comments to the MacMini mid 2011 guide there's an excellent tip in how get the SSD in place, by first attaching it loosely to the antenna plate and then use the antenna plate to manoeuver the SSD into position (the two screws on the thin side of the SSD must fit into two rubber sockets). Then carefully loosen the screws again leaving the SSD in place, and finally resposition the antenna plate.
I also thought about using a plastic suction cap on the SSD to grip it, but I didn't have one.
Very helpful guide, thanks! As many have said before, I would not detach the fan or antenna, just move it out of the way.
One very trivial tip: slide a piece of paper over the logic board as soon as you've removed the fan, as a protection against accidentally touching the components with your fingers or tools.
I did not reinstall the plastic cover on the HDD. This is only to protect the logic board of the HDD, which ofcourse is very well protected in SSD's.
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