Updated original post with the following
Update: March 2015
Chips has made a release of uae4all2 with PI specific code for scaling and vsync. Its currently the best way to enjoy uae4all2 on the Raspberry PI
http://www.raspberrypi.org/forums/vi...?f=78&t=102328
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if you already have a working version of uae4all2, copying the uae4all binary across to your current install folder and chmod +x should be enough (just remember to backup/rename your old uae4all )