"You are not talking to me clearly" is a fine correction. I believe the "not" has to be in front of the verb since it changes the action. - you are not going with me - you will not travel without him I canNOT think of a sentence in this format that the "not" would not precede the action.

It sounds very unnatural and confusing. The problem is that you've put the negative at the end of the sentence, when it should be near the front (within reason). "You are not talking to me clearly" is the best way of correcting the sentence. The other option is to replace "not clearly" with another word or expression. "You are talking to me vaguely." "You are talking to me in riddles."