Saying 'do I make myself clear" could sound quite severe, as though you are telling someone off. It might be better to ask, 'do you understand?'. If someone has done something against your instructions then you would probably tell them off and finish with 'do I make myself clear?', but I wouldn't start with that tone.

"Did I make myself clear?" Is correct. "Do I make myself clear? Would also be correct. But never "Do I made myself clear?"

I've heard people say: ¨does it make sense?" implying the same intention. It seems much more polite as you don't question the interlocutor's ability to understand.