1) As you can see from all my recent posts, I'm a newbie here too. So, I don't have much to offer here - other than pass along information from my recent threads: which is that the Surly Cross-Check, a wonderfully great bike, can be faster and lighter with select components. It fits cyclocross tires and fatter tires for harsher weather/terrain, so no worries for those unpaved paths.

2) Newbie = no training advice here.

3) I've never reached the point of sores, but I have been in serious pain that needs not to be detailed here. Like you, I've used tons of chamois butter - which didn't fix it. Due to the sensitivity of girly parts and other areas - I have tested many a bike short, and love the chamois' on the Izumi's...so I'd stick with finding the right saddle for your own issues. I finally found a saddle that deals with mine - and everything got better.

4) When I went slacker from doing my PT exercises (after I stopped seeing the PT), my knee issues came back. Maybe keep up with the exercises your PT gave you and have a professional analyze your cycling to see if there's something you can change in your stroke/positioning to ease the pressure on your hip and knee?? For me, my knees tend to go inward (or wobble side to side) and when I don't consciously fight to keep them straight in my pedal strokes - I always end up with knee pain afterwards...same issue comes up when I run if I don't try to keep my knees straight on each stride. Since you already goofed around with the cleats - I'd focus on your body mechanics and see what's going on there.

Good luck with everything!