I notice that in conversation lesson 2.1, the first sentence says "Kyoto-eki wa douyatte iki mas ka?" But in grammar lesson 2.6, the same sentence is rendered as "Kyoto-eki ni wa douyatte iki mas ka?" The translation is the same, so what is the function of that extra "ni" and why is it missing from lesson 2.1?

Sorry for the late reply. "Wa" can be combined with other particles, such as "ni", indicating direction, "de" indicating location and "kara" to indicate a contrast. (one of the main functions of wa in general). For example: Tabako wo sutte mo ii desu. : It's okay to smoke. but: KOKO DE WA tabako wo sutte mo ii ja/dewa nai desu. HERE (the contrast) it's not okay to smoke. Hope this helps. Just let me know if you need more explanations.

Pascal P shouldnt this sentence: KOKO DE WA tabako wo sutte mo ii ja/dewa nai desu be like this: KOKO DE WA tabako wo sutte Wa ikemasen

IIRC, both are acceptable. The "ii ja nai" means more specifically "can not do sth", as in not having permission.