1) No such thing as replacing back MC you took. They have to pay you for the MC days as long as MC was produced
2) No such thing as replacing back Public holiday given. Make sure they pay you salary for those days yeah!
3) They cannot NOT accept a resignation.
My advise, Serve your notice properly, wait till they release your salary payable IN FULL than leave. As long as you serve your notice properly, shouldn't be a problem
Just tell them you want to consult the labour office on the matters you mentioned, that should scare them enough!