Share your experience!
I know is too late, but if you fix it, my recomendation is to go to the magnetic cable for charge.
So you don't have to open it all the time.
I changed to that, and for manage pictures and music use WIFI connection.
Slow but work.
Regards.
Gustavo.
as far as you dont sure about water proffing better dont risk your phone
however you can contact sony here for information about repair or its cost
The cover can ensure waterproof mainly owes to the Silicon seal underneath the cover, if you are sure they are complete, your cover still works.
And if you still worried a lot, you can replace a new Xperia Z1 USB port cover by the video.
Good luck to you!