There should be an agreement between the subject and the verb, so the first sentence is correct. The verb 'have' follows the third person singular and is used in the present simple thus forcing you to use the verb form 'has'. If you want to put 'have' in the subordinate clause, then you have to reverse the order of the subjects there, like this: 'If your physician or you have any questions, please call us.
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ozzourti it sounds best when the verb is in agreement with the latter of the twoThis is, in fact, the "rule" for "or".