Can't help (don't have the i3 with MMU yet) but if anyone figures it out, I'd love to know about it - I am thinking seriously about getting one to be able to print different materials mixed, and I'd really rather use S3D than Slic3r. S3D produces amazingly good two-material prints from my FlashForge, and the idea of mixing four materials is very exciting!
Had some free time and dissected some Slic3r exported GCode and got the tool change script to work, but because it does a unload/load/wipe as part of the script, it creates a second prime pillar that's fixed in location. FFF attached here and also x-posted to the Prusa Forum. Use at your own risk!