Having the homeowner sign a waiver does nothing to get you out of Dutch with the state of Massachusetts. In Massachusetts, permit procedures and regulations are spelled out in the Building Code (780 CMR).
"A person who shall violate a provision of the Building Code (780 CMR) shall be punishable by a fine of not more than one thousand dollars ($1,000) or by imprisonment for not more than one year, or both, for each violation. Each day during which any portion of a violation continues shall constitute a separate offense."
You guys are fortunate. In New Jersey, they upped the fine to $2000.
So, again, having a waiver does nothing but confirm that you and the homeowner conspired to do the work without a permit.