'May' is asking permission. Using 'may' with 'go' would be OK if you are asking your parents or your teacher, but otherwise it sounds a little subservient, rather than polite. If you are at someone else's house, then 'May I use your bathroom' would be more appropriate. The 'I was wondering' form is fine. It is possibly a little too polite, but that depends on context. In Britain, that would be a good form to use, except for using 'bathroom' ;)

I would say: " would you excuse me" instead, or "will...... I wouldn't have mentioned "the bathroom" at all. I guess the first one may work as well (depends on the situation), but definitely not the 2nd one.

Not quite right. With indirect speech, the verbs all have to go one step back in time. For example : "Will you help me?" ---> I was wondering if you would help me. "Can I have a word?" ---> I was wondering if I could have a word. "May I go to the bathroom?" ---> I was wondering if I might go to the bathroom. Would anyone ever say that in the real world? No, nobody. Asking permission with "May I...?" is actually quite rare nowadays, and we never use "might" in this way any more. In modern English, if we want to ask permission, we use "Can I...?". To be more polite or tentative, we say "Could I...?". And if you want to be even more polite and tentative, we use ( as you suggested), the indirect question, "I was wondering if I could...." For example, you could ask your boss "I was wondering if could go home early tomorrow". Forget about "may".

If I were you,I would like to say: Mind if i go to the bathroom? or Do you mind if i go to the bathroom?