Hi
XYZ's software does muck around a lot. i have had stl files that ended up with holes in them or uneven layers after slicing was done.
Have started using slic3r as well, then used threedubber to get the files converted to .3w, saved on the SD card and printed like that.
have not done much printing with this yet as i need to figure out how to change the gcode to stop the printhead hitting the bed when it starts moving the first time, but you would have to change the print speed settings as the speed that it put in the first time was way too fast for the jr to handle, and the extruder kept skipping/knocking as the hotend could not keep up with the feed rate.
so what you would need is a .stl file to work from (keep a backup copy of your original somewhere save). during the slic3r setup process, enter your printers details, print bed size, nozzle diameter, etc as prompted. for gcode flavor i left mine on reprap for now. should be a good enough base to start from and experiment further with small changes here and there, and print to see the results.
there will be a steep learning curve but don't let that put you off. anything is better than XYZs crapware.
good luck