Training: add bricks to your workout routine. In other words practice the run/bike and bike/run (most important) stuff. You need to be familiar with that "wobbly" feeling. You can also practice transitions: changing from bike shoes to running shoes and getting your helmet on/off quickly.

Gear: I stick with bike shoes. I find the advantages of cycling shoes outweigh the transition time. Again, practice this switch in training.

Running in lightly-padded (or tri) shorts is way way more comfortable than trying to ride in running shorts IMHO. Running shorts tend to be waaaay tooo short and just kinda creep up and get really uncomfortable on the bike. Again: practice running in bike shorts in training.

Other things to consider: eat (gel works best for these short-distance events) and drink drink drink on the bike.