Yes, 'how long' can be combined with various types of VP. In fact, even (1) is possible (although it is most unlikely, hence your teacher's probably forgivable judgment), but only with a future reference, i.e. 'you have agreed/arranged with someone to wait for how long?'
Naturally, however, it could not meaningfully be applied to the present time: a question relating to someone's customary waiting time would be phrased in the present simple (How long do you (usually) wait?), while one referring to the total waiting time up to the present time of speaking would be couched in the present perfect progressive (...have you been waiting?)