I have never done one because my knees don't run, but friends who have say the transition itself is the most difficult (i.e., painful) part. They've said you really need to fit that into your training program.
On the shorts, can you afford (or already own) a pair of lighter tri-style or spin-style shorts? I would think a light thin pad would get you comfortably through a race of this length. Cyclocrossers wear padded shorts and they do plenty of running (and lots of transitions).