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are the audio files 320kpbs MP3s?
What if you transfer the files directly from your iphone to your computer to your phone without PC Companion or Media Go nor Xperia transfer
I can't content on number 1, but regarding number 2, sound quality should definitely not be affected by storage location. Digital music is data, and the player is reading it the same way regardless of location... It should sound the same even if it's located on a USB flash drive using an OTG cable...
I have similar problems with my brand new Xperia Z3 Compact and a Tunelink Home (see http://www.newpotatotech.com/TUNELINK_HOME/tunelink_home.html).
There are distortions which sound like high frequent dropouts and changes in playing speed.
With my older tablet (Acer A701, Android 4.1) and the same sound files, the same player software and the same Tunelink Home device the sound quality is great.
Wifi on/off as well as reconnecting bluetooth connection does not change anything.