Just realized that many people had the same problem. If I read the comments too, I would have saved myself a lot of trouble :). But at least we have a plausible reason for the described behavior: the position matters, and OS X may try to handle the 2 drives as one Fusion drive (and somehow fails at that). Maybe it's a setting issue, or just has not been tested this way. Consumers should not upgrade to SSD by themselves :).

I have followed the good advice here on upgrading a 2013 Mac Mini (500GB) to SSD.

However, on step 37 I disagree. What happened:

- I had OS X Maverick on the original 500 GB HDD

- installed the SSD in the "Upper" position, as in the figure

- left the original 500 GB drive in its original, "Lower" position (meaning upper when the Mac is upside down)

- followed the steps in 37

- install was terribly slow, ~6 hours; there was some data corruption, the SSD would not boot; I tried to fix permissions, disk etc, no help; benchmarks showed slow read with normal write speed; after a while there was an error about the SSD could not be repaired and it disappeared (unmounted)

- at some point I've seen some complaint about Fusion drive. Then l realized that is it possible Maverick tried to treat the SSD + HDD as a single fusion drive?

- switched the positions of the HDD and the SSD, so now the SSD was in "Lower" position. Also moved the protecting/insulating sheet to the SSD.

- Now everything works. So, position matters!