My supervisor and head of center is doing unethical things and I am in the middle Slowly but surely my supervisor's behaviour has escalated. It started from unreasonable, to downright unethical.

My university complies to the Vancouver autrhorship protocol, yet my supervisor/HoC has made his own guidebook regarding who is author and when. Something along the lines of "Student, Actual Contributor, Cosupervisor, Supervisor, Head of Center". Which implies that he is on every single paper. In my papers and in my work in general, though I always inform him and invite his contribution, he never really does anything more than "give comments" which are surprisingly all clustering in introduction and conclusion. When I am finished with my PhD, I need to submit a form for every paper I've published and state which of the coauthors have contributed in which way. This is a direct clash with the University rules.

He also overrules the PhD school, even when he simply cannot. My Mid-PhD evaluation report is now 3 months late, but "who cares, they are super rigid anyway".

There are many examples of how his way of doing things does not comply to actual rules of the institution, and it is putting me in very bad situations both with other authors but more importantly it is impending my progress in my PhD project.

How do I raise these issues with him without being the black sheep that has a problem with the way he does things? It's my impression that the university's rules were put in place for some reason. I've informed the vice-dean of these things and it is being looked into, but in the mean time there are deadlines that I cannot afford to miss - a PhD is a time-constraining thing. Is there any way possible to bring to the table my honest concerns without implying that what he's doing is immoral and incorrect?

After all, I'm a lowly PhD student whose credibility is worth nothing compared to the HoC. I don't want to become a target.
Sorry for making an answer, but still without enough reputation to comment.

That is a very tricky situation, I can imagine, even more because you have colleagues that simply don't care. I see that the question is already one month old, but I just wanted to point out, in addition to the other comments, that sometimes universities or departments have some sort of complaint and review procedures, rather than just send an email to the dean. 

I would just like to also add that I hope you don't give up on trying to make academia a "better place". Academia is full of people that are "untouchable", and if no one complains, it will stay like that forever. I wish you good luck and if you found some procedure or detail that might be useful to others in the same situation, it would be great if you can write them down here.