..wait a while before you order new boards.. it could be more to fix there.. P.
PS1:
-what I generally miss are the pullups on the sdcards pins like CS, datain,..
-pullups on the carddetect, writeprotected..
-add the sense (carddetect) on the microsd as well (and the pullup)
-add pullups on any RX, RX1 and alike lines which may float when the cable is not connected
-I would not use A7 for WP of sdcard1 but for cardetect (sense) of the usdcard
..maybe more
-try to load the power supplies with a few hundred mAps (when applicable) and see if it works stable (when inserting sdcards, when formating sdcards, etc)
- I would add few 10-20uF ceramic caps to the sdcards vcc33
PS2: did you ever put a shield into this Mother of all boards?
If I were you I would assemble one more board and ask somebody to use it intensively for 1-2weeks in some harsh environment (various shields etc.). Then I would consider the second batch.. Moreover, you planned only one sdcard, did'n you? 