What exactly is wrong with the default start gcode and what are you trying to change it to? We've done extensive testing with our own Flashforge and it works fine.
Why are you trying to change the config file instead of editing the start gcode from within MatterControl itself? The settings in /usr/lib/MatterControl/StaticData/PrinterSettings/ are the default settings loaded when you add a new printer. Your own settings are stored in an SQLite database in ~/.local/share/MatterControl/ (in 1.6 these will be moved to .json files)
Slic3r and Cura engines are disabled for dual extrusion printers, since MatterControl currently does not support dual extrusion using those engines. I realize its a little confusing to have them completely hidden in the menu. If you want to try Slic3r anyways, switch your extruder count to 1.