I've spent a bit more time poking and I'm afraid that there isn't much good news.
Firstly, it looks like there is a fault in the plexi volume pot, which is rather frustrating since it's a difficult beast to get hold of. Truth be told however, it isn't actually quite the right part. The design called for a 1M ganged audio taper pot... and all I could find was a 500k version. This is the dodgy pot with the 7mm thread (designed as a blend pot for bass guitars apparently, hence the mid point notch... actually, that might mean that one of the tapers is a reverse taper anyway... which might explain the 'hotness' of the parallel mode. I'll need to make a plan to find an alternative.
It also seems that the state of the plexi tone control, especially the bass knob, has a marked impact on the black face circuit (although, this really isn't a surprise). In the short term I'll live with it but I'll need a plan to overcome it. Truth be told, I anticipated this problem up front and sort of hoped it wouldn't be too bad, so it's not a massive surprise.
Basically, I see two options. Either put buffers between the outputs and the phase inverter (probably in the form of cathode followers... but I'll need to look it up), or change the switching arrangement so that only the active channel hits the phase inverter. This would probably mean getting rid of the rotary switch and adding a set of toggles, one for each channel. The first option is definitely the most complicated and I'm a little nervous about it colouring the sound somehow but it is quite nice and neat once it's in... plus the extra tube is cool ?. The second option is more flexible and easier to pull off (except for the additional chassis work) but is quite a fiddly thing to operate... i.e. probably fine for me, but a mess if anyone else tries to use the amp.
I'm going to have to do a little research on this.
Last point is that the plexi channel is still WAY louder than the blackface channel. I think the easiest may just be to put in a voltage divider at the output to bring the volume down a bit but I don't want to mess with this until I have the volume control sorted out.
EDIT:
AAAAND there it is. The offending pot is an MN taper, which is completely different to what I need. I'm a little grumpy since it was listed as an audio taper but there ya go. Definitely going to need to source a replacement.