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.
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