OK, 8 hours running at '5' on the volume control, mix of guitar loops and random music and the results are in.
I recorded the amp with the H1 before and after playing the same tunes, one on setting 22 (65 twin with reverb), and one on a JCM800 type of sound I set up myself. I loaded the audio into Reaper and used the SPAN spectrum analyser to see what was going on.
In short, yes, the frequency range did become a little more evenly distributed and even slightly extended at the low end - but, and it is a big but, the peaks remained unchanged in the 800hz and 2-4khz ranges, which means that the sound is still painfully toppy.
I also tried the amp by disconnecting the speaker and running through a 100w passive wedge monitor loaded with a Fane full range 12" driver. Still uncomfortably shrill. This monitor has been used at hundreds of gigs, often flat out, so it's definitely run in.
Conclusion: the power stage of the Mustang 3 is seriously biased to higher frequencies, slightly disguised by the Q around the 800hz which adds some high middle, but lacking in low end response. Unforgivable really
So I won't bother replacing the driver, but will use the amp with a pre-amp/multi FX pedal set to deaden the nasty spikiness in the sound (I use the 'empty' preset available from Fuse when running pedals through it), and reset all the amp models to take out as much of the overbearing high end as possible without losing the brightness on the Fender models.
Work for another day!