I'm not the best scripter in the world so I didn't include the GECK portion of mod conversions in my tutorial. Most Non FOSE mods will convert just fine with out having to open the GECK.
Don't use the "Recompile All" button EVER!
When saving a script it get's recompiled so when converting FOSE mods you'll need,
NVSE installed
GECK Power Up (Running with NVSE)
After you have ran through the basic conversion process (Explained by my tutorial) you'll need to open the mod with GECK Power Up and go through all the scripts that the mod has added. Opening them and saving them again. there may be errors due to changes between NVSE and FOSE. These errors will need to be resolved for the script to save and recompile. This is where some understanding of scripting is needed.
