I wish I could get my wife onto a road bike. Well, she is but just with goofy riser bars so she doesn't have to bend over.
The comments on women's specific bikes beg the question. How did she like the fit of the Trek? Is she as capable of bending over to the bars today as she was when the bike was new? Did she like its handling - i.e. does she like American style geometry or does she pine for some Italian bike she had before the Trek? I've owned many good bikes over the years but keep coming back to Italian ones with American ones (lastly, a Parlee Z1 and Z4) feeling "different" in a way I didn't find as comfortable.
Re wheels. Why would she want carbon wheels? Is she trying to beat you? Does she want to fiddle around with tubulars or are you or your dad going to pick her up when she has a flat? I've tried carbon wheels (a whole season on my #1 bike) but just don't find the braking power and, for tubulars, gluing hassle, worth the trade-off. I just keep coming back to high quality aluminum clincher rims. And remember that if she's light, wheels like Ksyriums may seem really rough compared to her old 32 spoke clinchers.
Lastly, if she liked 9 speed or whatever it was (maybe even
Record, why switch to DA unless you go to Di2?