Okey, now it official.. I'm going crazy..
I now have my Apple Universal Dock (w/ IR) back together, in one piece and without left over parts ;-)
Connected it to my iPad3 (30pin connector) via the prementioned (see link above) extension cable and it works just fine!!
Play/pause - stop - previous/next - volume control ALL WORKS. (where before it didn't!)
So for everybody out there, you CAN connect an iPad to a Apple Universal Dock (w/IR) via a extension cable and use your (music) IR functions!
I'l try more apps as we go and keep this thread updated...
APPS that DO work w/ IR remote control via Universal Dock on an iPad3:
the following functions where tested: play/pause, previous/next - volume and work just fine
Apple MUSIC
Apple PHOTOS
Apple VIDEOS
Djay (Algorhythm)
Spotify
APPS that DO NOT work w/ IR remote control via Universal Dock on an iPad3:
DJ Rig (IK Multimedia)
KEYNOTE (Apple)
This is how it's set up:

Link to extension cable:
http://www.amazon.com/Connector-Extender-Extension-Cable-iPhone/dp/B004BJLXAM/re f=lh_ni_t?ie=UTF8&psc=1