"Is that you?"
Translation:To jsi ty?
I saw "Jsi to ty" around, so I suppose the word order is somewhat flexible right? Are there any rules or guidelines for word order?
The word order is very free, but not completely. It cannot be treated here. See the recommended resources like the Tahal's book.
Correct, but this is quite a special kind of sentence. Normally you couples with are, not is.
No, that is impossible. The "je to"/"to je" is used for any gender, but it must be the third person, it must be compatible with the "je" third person form of the verb.
Jsem to já,
Jsi to ty.
Je to ona.
Jsme to my.
Jste to vy.
Jsou to oni.