is there an option that allows for the autoresponder to attach a unique number or identifier visible to both parties in the autoresponder return message
Just to provide a little more detail, you'll probably want to use the: %%RESPONSE_ID%% alias, which provides a unique number that can can identify any response in FormAssembly. Note that this value is used throughout FormAssembly, so the values your responses receive will be non-consecutive but steadily increasing (monotonic increasing).