Two of the biggies for me were IFR Communications, and developing the instrument scan. It took a while, but eventually it all clicked.
If you're near a towered airport, pick up a scanner and listen to as much as you can - Clearance, Ground, Tower, Approach, or try one of the ATC online web sites.
I don't recall my CFII teaching the "scan" (he probably did-I was too dense). It becomes second nature at some point during the training. Making sure the 6 pack agrees (assuming steam gauges), and getting a look at the engine instruments every so often, etc
Don't fly an airplane with an ADF

The VOR beam is wider the further out from the station you are