CDNpielover, you nailed it! Looks great! Way to go!
As far as the browning bottom goes, yes, that all comes down to your local conditions of your oven. I am totally sold on the two-stone method, start high and finish low (if needed), as the lower stone browns the crust whereas the top stone cooks the cheese and sausage more.
All that being said, the pictures look like the correct amount of browning. Use less bench flour, if you can, and that will also improve browning. Furthermore, if you changed nothing and just left it in longer, you may have gotten the crust more to your preferences and browned the cheese, too, which is appropriate to style. I never pull a pie before the cheese is at least a little browned--or a lot!
Indeed, the sauce is fennel heavy when tasted plain. I have a buddy who uses this leftover sauce as a base for pasta sauce, but I do not like it that way at all. IMO, it is strictly a pizza sauce. It just works...sum greater than the parts and all that jazz. Looks like you discovered that yourself.
As for the size of the sausage, it is perfectly acceptable for Chicago thin to have big knobs of sausage on there. Or go with whatever size you like. I would say to flatten them out when they're that big--make 'em less like meatballs in that regard. BTW, how did you like the sausage?
Man, I am totally honored that you made this pizza true to type, even down to the homemade sausage.
Cheers to you, sir! Hope you make it again and again.