Looks interesting.
A few things come to mind:
1. Set Audyssey aside for now and get things as good as possible without Audyssey. Otherwise you are chasing your tail.
2. Yes, run one speaker at a time when measuring to see what's going on. Later, you will run sub(S) + one speaker.
3. It's okay if you want to measure full range for now, but ultimately you'll want to do bass management right, cross over to subs, and tackle room modes, so don't worry about things in the mains that look wonky below 100hz. Setting up the right crossover settings (not just frequency choice, but distance/phase, etc) will let you address that:
and
4. It wasn't clear to me where that dip is from the diagrams since most are not un eq-ed but it sounds like SBIR may be the culprit. Moving the speakers as close as possible to the front wall, placing thick acoustic treatment directly behind them, and re-measuring to confirm that solved it will tell you more.
4. I don't see a layout, diagram or picture of your room. That plus measurements would help other folks advise you on what else might be useful.