It depends on whether you are talking about your own school attendance as a pupil, or going to schools to work or for some other purpose. If it is your experience as a pupil then ‘I used to go to elementary school but now I go to secondary school’. If you are a worker at school or a visitor for some other reason, then either of the two examples you give could be used, depending on the context of the statement. I have been doing voluntary tutoring in schools. I could say. ‘I had been going to a secondary school but now I am going to a primary school.’ If I had only recently switched then I might use the present perfect ‘I have been . . but I’m going . .’

I’ve Been going to elementary school is OK but it would probably be better to say: -I went to elementary school OR I used to go to elementary school but now I go to.....

As per my understanding, this is a situation when one has newly enrolled to a secondary school. So it's okay to go with, I have been going to middle school for the last __ years and now I'm going to a secondary school. (Expressing your amazement, excitement of anger for this change)

Zweite Satz ist korrekt. Wenn du past perfekt benutzen willst, sollte beide Sätzte im Vergangenheit sein.