You could record the stuff you want to record into two table/record object. It will be recorded as .raw format, but you can easily convert it into wav by using Audacity, which is free.
Playback audio from Axoloti is limited to 4194304 samples = 87,38133333333333 seconds in one file.
But I am not sure if there is a limit to recording, havent tested it.
The recording part of the Axoloti patch could look something like this:
Both recording tables are started with the same button, so you should be able to compare them pretty precisely afterwards.
The tables sizes used are 2097152 samples long at 48khz sample rate, which is equivalant to 43,57816666666667 seconds. So recording in this setup is probably limited to that length. But I think you need to test this yourself.
DISCLAIMER Havent tested this exact patch, but I am pretty confindent that this set up will work
(Ps. You mig