-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?,..
@pito, Turns out I Don't have pictures - only a shortcut to a desktop folder! Blew that one. Will get them soon.