So I looked at your post on the Cyclops and I have a few questions:
Instead of using that firmware "redirection" couldn't you simply wire the thermistor to both the pads (E0 & E1)? Also you could leave the heater pads empty. I don't think the firmware can detect the lack of resistance, so it would think it's working as long as it gets a signal from the thermistor.
Alternately, you could drill holes into the opposite side of the heater block for the heater cartridge and the thermistor, effectively creating a "redundant" system.
I noticed you were printing a skirt as a means to waste the blended color filament. The problem I see with that, is that on a small model you might not waste enough mixed color filament out, whereas on a larger model you might waste too much. Why not figure out how much filament extrusion is needed to get rid of the mix and get a pure color, then create a "waste tower", a hollow cylinder or rectangular pillar that prints enough perimeters to account for the needed extrusion length. You could add that tower to all your prints and simply scale it vertically to match the height of whatever model you're printing.
Another question. in a given layer, does it print everything in one color then switches to the other, or does it alternate back and forth between the colors? The waste tower does NOT make sense if it does the latter.
Anyway, I do like the idea of the single output and alternating feeds, no wasted build area. Primarily I'd like to get it so I can print PVA, but I'm sure I would print in dual colors as well.
To print or, 3D print, that is the question...
SD3 printer w/too many mods, Printrbot Simple Maker Ed., FormLabs Form 1+
AnyCubic Photon, Shining 3D EinScan-S & Atlas 3D scanners...
...and too much time on my hands.