If pickit3 serial# is listed in project properties, it is seen by MPLABX (you can verify- disconnect pickit3, open project properties- pickit3 will be listed with no serial#).
Your previous errors indicate MPLABX is not communicating with the pickit3, but also note there is a setting in the project properties for the pickit3 to provide power to your circuit- if you are using the pickit3 to provide power and have not enabled that setting, MPLABX will communicate with the pickit3 ok but the pickit3 will complain that it can't talk to the chip (which does not appear to be happening to you, yet )
I would disconnect the pickit3 connections on the 6pin header, then try to program- it will fail of course, but you should see communications happening between MPLABX and pickit3. (I'm not sure what, if anything could go wrong if connecting the pins incorrectly, but this would eliminate that possibility).
You may need to Google 'PICkit3PlatformTool' (part of your error message)- I'm sure you are not the first with this error.