Burn bright, burn blue.
I had a similar experience, but when I realized the two 5.0mm T8 Torx screws were 2 of a set of 3 that also served to hold the cover on, I wasn't comfortable with only securing the cover with 2.
The "engineering tolerances" are definitely tight for the AirPort antenna plate. I would recommend trying to replace it as soon as it's removed for the first time, in order to work out the (precise) alignment of it.
Nothing I tried (including the suggestions here) seemed to help me during reassembly. No matter what I tried, I couldn't get the holes for the two 5.0mm T8 screws to line up. Eventually, I had to resort to CAREFULLY and SLIGHTLY re-bending the curved edge of the antenna plate.
It may just be my own experience, but the hard drive connectors appear to be "sensitive" to ANY pressure, even when (re)connected properly. I found that I had to repeatedly re-seat them when re-installing the drive, AirPort antenna, and cowling. I would recommend holding off on putting the screws back for the AirPort antenna and cowling until both are in place, and re-checking the hard drive connectors before installing/tightening those screws.
During reassembly, watch the power harness and connector from the power supply when reinserting the logic board assembly into the case. When the board is close enough for the connector to reach, re-attach it before inserting the board the rest of the way. I found that if the connector is lined up properly, it almost attaches itself.
Also be careful of the hard drive and IR sensor connectors.
During reassembly, after putting the "lower" drive back, test fit the AirPort antenna to make sure the two holes in the antenna plate line up with the two holes in the drive. If not, check that the power harness from the power supply is routed correctly. If the power harness is next to the power supply, go back and re-route it properly.
When putting it back, make sure that it's both in the correct place and fits properly; otherwise, it may come loose. After reassembly, if you hear what sounds somewhat but not quite like a loose screw rattling around in the case, it's probably this clip.
Don't worry: it's only 20 steps to get back to it. I hate this metal clip. ;-)
Specifically, note the power harness and connector, and that it's routed "above" the inner edge of the power supply ("below" when viewed from this angle). That power harness needs to be in the same position when replacing the power supply during reassembly. If the power harness ends up next to the power supply instead, the "lower" drive won't fit properly and the AirPort antenna won't line up correctly.
With virtually everything removed from the outer case, this is a good time to look toward the front of the case to notice the two locations where the standoffs from the "lower" drive normally fit. You'll want to be aware of this when reinstalling that drive later.
The ribbon cable with my kit was already bent correctly when I received it. Not sure if it was just that one or if they're all going out like that now, but it saved me a few steps (and worries about ruining the cable). Thanks! :-)
A few general notes from my successful effort; I'll leave step specific comments where applicable.
First, the kit is overkill IMHO, in that I already owned a suitable multi-piece Torx driver. I'd like to see the kit offered as parts only sans tools; however, the current sale price (as of this writing) does make the inclusion of the tool kit a good deal.
Second, "pay attention" to how your Mini is set up both before and after. I was using the "Apple Mini DisplayPort to Dual Link DVI Adapter" to connect an Apple 30" Cinema Display. Before I started, both the mini DisplayPort and USB ends were connected to the Mini. When I finished, I overlooked the USB end and then proceeded to have my own personal "doh!" moment trying to figure out why I wasn't getting any video. To make a long story short ("too late"?), after re-connecting the USB end I had video again (and an audible sigh of relief).