Dual extrusion is working! Through the magic of Git, I have managed to combine a firmware that handles multiple extruders on independent axes with my firmware that does the bipolar conversion. Amazingly, the thing compiles and runs. I reworked the way Marlin stores the current position in both coordinate systems internally. The way it was doing it before was confusing me and causing bugs while homeing. Also had to add support for multiple sets of endstops per axis. For more details check the github. 

First dual extrusion test prints are promising, but clearly a lot of work still needs to be done. Definitely need some way to clean the extruders when switching between them. Having flashbacks about dealing with oozebane in skeinforge. No cleanup was done on these aside from removing whatever excess I could with my fingers.