Have you taken the Temperament quiz yet for your DD? If she's spirited she'll require kid gloves to help her wind down for naps and bed time.
I don't think any of us answered your question regarding waking her from a nap. I think at this point you should let her take a nice long nap if she wants it. I would wake my boys by the 2.5hr mark but otherwise I just let them sleep. They need so much rest at this young age, and it gives you a mental break as well.
Crying is ok, as long as she's not left alone. Almost all babies cry because it's their only form of communication so it's not that you're aiming for absolutely no crying at all, just no CIO or CC. She will cry when you change her routine but if you or DH is right there to love and support her, it will be a cry of frustration, rather than a cry from abandonment.