I know for me, squats are a definite no-no. I had a problem in my right knee (plica band) a few years ago and ended up having to have arthroscopic surgery. :-( One thing the dr. told me NEVER to do was squats. I don't know why, but they are the one thing that always bothers my knee. Every few months I'd think, ok, I feel good, I'm going to try them again. Without fail, my knee would be really sore for several days after. I just don't do them anymore.
That being said, I think any one of the things you mentioned could be the culprit. As usual, you've gotten some good suggestions here (this forum is great!). Experiment with different things. I think lowering the step height is definitely a good idea. 14" is high, especially if you're not that tall. The highest I ever go is 12", and I still feel like the muscles get worked really well. There was a good suggestion on the lunges, too. I think static lunges seem to be the least dangerous. I can do those, but I stay away from the low-ends. They definitely bother my knee. Try modifying each move a bit. If you're still feeling sore, try eliminating each one, but one at a time. Once you start feeling better, you'll know which one was to blame.
If you do find there is one move that you just can't do without discomfort, you can always find modifications. Since I can't do squats, I do leg lifts, which really work the quads well and actually make my knees feel better--very strong. I don't have a leg lift machine; I just sit in a chair with ankle weights on and do them that way.
Good luck!
Marie