Your mason is wrong and this chimney will never pass a code inspection.
First, footings for foundations must be level and stable according to building codes.
Yours is obviously not.
Second, wood burning stoves require stainless steel chimneys not masonry chimneys. Or a masonry chimney with a stainless steel flue liner or a continuous approved masonry mortar specifically designed for use with wood burners.
Before you do anything, have your code inspector out for his advice.
It appears from here you need to fire this mason, then demolish the chimney and start over.