Both issues have disappeared.
Things i did (not in this exact order):
- Reinstall the app (this didn't seem to fix the issue right away)
- Logged in to my rekorbox/pioneer account in the app
- Synced 2 playlists from Rekordbox (Mac OSX 10.13) over Wifi
- Shut down Rekordbox on Mac
- Switched XDJ-1000's of and on
- Connected the old Rekordbox iOS app to the XDJ's (it was after this that Wifi connection started working for the new app)
I'm not sure if any of of the above actions helped or if it was something else bugging the connection. But it seems to work consistently over Wifi now (With AIFF's, finally!)
It seems the Wifi playlist sync issue is related to the fact that the App is not staying connected in the background. At least it worked when i kept the app active during the transfer.
I couldn't get the wired connection to work over USB, but that might be the cable i'm using (somewhere in the manual it states connection over usb or utp is possible)