Enter EC pedals and their Super Switcher, there are a lot of switchers on the market, after some consideration this is the one that suited my needs best. Using 1/4" cables I can control the Mark V's channel switching, solo boost and EQ. The reverb can only be controlled with the V's foot switch, so I added a TC Electronic Hall of Fame reverb, good little pedal, very versatile. The switcher has 8 loops (1 is stereo) but I'm only using 7 of them. There are 3 banks of 7 presets each. 21 presets is more than enough, in fact when I sat down to program my presets, I found it was easiest to program presets 1,2 and 3 identically on all 3 banks. Those are the core rhythm sounds. Presets 4,5 and 6 are lead sounds using the amp's Solo function and various combinations of pedals, for example all the rhythm sounds use the Xotic EP Booster and the ISP Decimator, the lead sounds keep the EP on but turn off the noise gate. On all 3 banks I set up preset 7 to be a manual switch for the Delay pedal, as I need to punch in the delay when using both rhythm and lead presets.
Bank A uses mostly channel 3 for one band.
Bank B is mostly channel 2 for the other band.
Bank C is set up for jamming, writing etc, the first 3 presets switch the between the basic rhythm sounds, then the remaining switches are set to manually turn on/off the solo boost, reverb, phaser and delay.
The pedals appear in the chain in the order of the loop they are in, all are bypassed when a preset doesn't use their loop.
Loop 1: Xotic SP Compressor (cleans, some lead presets)
Loop 2: MXR Phase 90
Loop 3: Xotic EP Booster (almost always on)
Loop 4: Fulltone OCD v4. (a little extra grit for some lead presets)
Loop 5: MXR Carbon Copy
Loop 6: TCE Hall of Fame (cleans, some lead presets)
Loop 7: ISP Decimator (noise gate, off for leads, rhythms need to be tight, I like leads noisy)
Loop 8: empty
The TCE Polytune is in the switcher's Tuner out and is bypassed until the mute button is selected. Further the entire board can be bypassed or the presets can be ignored and the loops can all work manually if needed.

Thanks for reading