I'm an NYC resident who visits Chicago 3-4 times a year.
Are you already on a wait list for Alinea? I like WD-50 here in NYC, but I LOVE Alinea. They probably have a list a mile long for end of June, though.
I'd also take her for drinks at the Aviary, at a minimum. Nothing really like that in NYC.
I'd focus on non-taco Mexican in Chicago and skip Big Star, to play to Chicago's strengths (my last visit to Big Star wasn't that great either).
Consider a Rick Bayless restaurant, as well. We try to fit one in on every one of our trips to Chicago.
Birreria Zaragoza, Cemitas Puebla, etc. sound like good calls, too.
I haven't been to Katy's but it appears they specialize in dumplings and noodles? If the chef spends a lot of time in Flushing (Golden Mall, etc) or Chinatown (Sheng Wang, Lan Zhou Hand Pulled, etc.), it may not make sense.
The pie places sound good to me -- there's only a few really seriously good pie places in NYC (Four and Twenty Blackbirds).
Thai is probably unnecessary if she does Sripraphai, Chao Thai, Ayada, Thailand Centerpoint, or Zabb Elee frequently.
There's actually three Yunnan restaurants in NYC now. Yunnan Kitchen, Yun Nan Flavor Snack, and Lotus Blue (more upscale, Yunnan-inspired). Depends if she has already visited them, I suppose.
You can get Eastern European pretty easily in Greenpoint (Lomzynianka is a popular foodie destination). I'd skip this in Chicago.
I think Hot Doug's is definitely more unique, along side Chicago style pizza, Italian beef.
BBQ, Ethiopian, and Indian might be too, good. NYC is not especially strong in any of those.
I'd skip Spanish. There's very good Spanish tapas here now with Txikito, Tertulia, Casa Mono, Boqueria, etc.