For the late 2012 model at least, when re-assembling, make sure the edges of the plug are lined up with the innermost grooves in the case (there appears to be another set that is closer to the outside of the case).

Careful when reassembling. Don't make the same mistake I did by attempting to screw in the hard drive bracket without having the power supply re-inserted and aligned. Otherwise the screw will end up in the piece attached to the bottom of the case (where it's not supposed to be) and you will have no choice but to pry the glued part off the case to remove it. If you start to hear a "crunchy" sound when screwing, stop immediately because it's probably a glued part coming off.

Same here. I basically had to turn the Mac Mini completely upside-down (hence, "right side up" from the normal operational standpoint), then gently move the drive pins into place against the side of the case. Once they went in, then the antenna plate screws lined up nicely.

That is true if you do not need to remove the logic board (i.e. you are only replacing the drive in the original slot position).

You can definitely omit the logic board removal if you are ONLY replacing the drive in the "old" (i.e. closer to opening) slot and not planning to put anything in the "new" (buried) slot.

OK, I should have read through all the comments before going ahead with this. I have a Mac Mini late 2012 i7 with 1TB HD. I wanted to add a Samsung 840 256GB SSD. Initially, I installed that drive into the open bay as described in this guide, but it didn't work. Disk Utility saw it as a broken fusion drive (as outlined elsewhere). So I removed the original hard drive, leaving only the SSD in the new slot. This also didn't work - internet install of OS X failed multiple times and the machine was extremely hot. I finally got it to work by 1) taking original HD cable and putting it on the SSD, 2) installing original HD into the new slot using the iFixit cable (but leaving it unplugged from board after reassembly), 3) installing OS X onto the SSD which is now sitting in the old slot with old cable, 4) reconnecting the old HD/new cable to logic board, 5) restarting and using Disk Utility to reformat old HD. iFixit really needs to update this guide to indicate the SSD will probably not work in the new slot!