I had this -54 error when trying to sync my iPhone 6s. I have no idea what changed between now and the last time i synched, except I did upgrade to 9.3.1 on the phone. I tried turning off and on my phone, tried to delete iTunes .xml, but it does not use an xml file anymore, I logged into iBooks on my iMac, and none of that worked. I decided to log out of iCloud on my iMac (that took some waiting, in Syst. Prefs), then when I tried to log back in it wanted a password with a capital letter, which my old pw did not have. So I reset the pw, jumping thru the hoops to do that, and had to re-login on my iMac and iPhone. Then I tried again to sync the phone to iTunes and it worked! Weird part of this was that Apple also wanted me to enter the new pw for my OLD Apple ID, which I thought I had deleted! So I just hit "cancel" when that window came up, and like I said this iCloud logout/ password reset reset worked for me.