SunShine won't run on roms with xposed installed, however it cleans itself up entirely after the fact and shouldnt be causing any issues.
s-off does change how a long of things behave, perhaps xposed isnt cooping well with that.
Can you verify with someone who has used a javacard or has factory s-off device?
Verified with someone that has factory s-off device. Xposed doesnt works for him. Working on getting you those files you need.
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