Replace the splash-proof micro-USB connector by a water-proof IP67 model
A new model of water-proof micro-USB connector is
available:
http://www.selectronix.co.uk/series.asp?did=277&sid=426&campaign=wizemail&dm_i=KF3,2MTDM,44SQXT,9MDU8,1
It might simplify the case sealing (no need of an extra joint around the connector).