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...does he have a case...?
He has enough to file a lawsuit and get past a Motion to Dismiss
or some other type of dispositive motion. Technically you aren't supposed to stop payments on a check once you send it, unless it was a mistake like sending $3000 when you were supposed to send $3000, or something like that, and you're not supposed to make deductions that weren't agreed on with the other party.
The way it is supposed to be handled is to either pay the bill and file a lawsuit OR file a lawsuit and have the judge determine the correct amount.
He is now stating the toilet he removed was not included in price after the fact and after we agreed on an amount he keeps adding after the fact what can I do?
File the lawsuit to have the judge determine what is actually owed. That is really the only way to determine everyone's rights and what is owed. Due to the amount the small claims court is the best place to file but since it is a contract
dispute you do have the alternative of hiring a lawyer to handle it and then suing for his attorneys fees as well as the rest of the damages and the findings you want.