How do I go about if I am in a temporary marriage but we wish to make it permenant, do we have to wait till the end of the contract on the temporary one or end it in a certain way? Or can I just do a new kutbah and say the formula for permanent marriage?

You must first terminate the temporary contract, giving it the rest of the term, by saying to her: I give you the remaining time, and she says, "accepted", and then you hold a permanent contract for a new dowry."