Sadly, I think the L-word is creeping into flight instruction.
I went to different places on my XC's. Dual, went to MWC, then PVB; after some solo XC's we went to GRB at night. Solo, went to RFD, OVS, OSH+ETB for the long one, and then went to OSH once for fun (requirements were met, I met a friend of mine up there).
Depends on the student, too. After I'd been flying with my primary CFI for 10 hours or so, I'd show up for a lesson and he'd ask, "So, what are we doing today?" He really let me take charge of the process, which was nice. But, I'd been obsessing about flying and flight training for about a year and a half before I had the money to actually do it so I had a good idea of what needed to be done.
Kimberly, great write-up! Sounds like the flight had exactly the intended effect: It threw some problems at you to solve, and you solved them and learned a few things along the way. That's what it's all about.
As I think you know by now, the transponder thing was simply a lack of radar coverage at your altitude... FWIW, when I flew through that area about 3 years ago the coverage was good at 7,500 feet but I'm guessing you didn't have any reason to be that high on a relatively short trip and were lower.
I'm curious, what model of radio were you having problems with, and do you know why it would only tune the nav side? That's a problem I haven't encountered yet.
Have fun - It keeps getting better!