Magnetometer coil equalization
I would equalize both channels.  The most robust method is to cut both back to a lower bandwidth.  Then you only need to equalize the gains.
Assuming that your scanning by hand a 1-2 second sweep rate seems reasonable.  Unless your imaging, you can narrow the sweep down to smaller distances when a signal needs investigation.
A 10-50Hz bandwidth should accommodate human response times.  In this case you can use simple "RC" filtering to a fixed standard on both samples.
You mention construction variations; so first, you need to buffer yourself away from the coils.  Then apply a fixed RC filter.  Since you have isolated yourself both in time and impedance from the coil variations you have complete control of the balance between the two sides.
Of course, this might all be done in software but make sure your A/D has sufficient resolution (time and amplitude) and compliance.