First, if U2 is an adjustable v.reg, then you certainly have the schematic wrong - the
arrow means nothing to me, you need 2 resistors. I would rather use a part with fixed
output 3.3V voltage. Also, do you mean to have a DOT above C16?
Secondly, you might try to get the people from the Arduino DUE development team to
review your design, as they would know the specifics better.
Thirdly, don't buy 1000 boards initially. Buy a few prototypes and test it like crazy. I know
a guy with 5000 useless pcbs in his closet, with a small but nasty layout error.