From my past Xperience (Experience) from fixing Sony Xperia Z, Z1, Z2, Z3 phones. I can confirm that there are two microphones inside the Sony Xperia Z3. One is together with the headphone jack and the other is together with the long black ribbon cable that is connected to the power, volume up + down.
In this case your bottom microphone is probably damaged then you tried to pry it up. You will need to buy another microphone + volume up + volume down flex cable to fix this problem.
You can buy it from eBay here:
http://www.ebay.com.au/itm/OEM-Sony-Xperia-Z3-D6653-D6603-D6616-Volume-Button-Power-off-on-Mic-Flex-Cable-/161886373220?hash=item25b12e0564:g:OkwAAOSwcdBWRaRP