I hope you got the issue resolved. Thanks to tdunham for trying to get you sorted out. There has been only one other reported issue with the mod and it involved a FC on a couple apps. The poster never reported back on the resolution You stated that your having issues downloading roms and the like. Is it possible that your downloads may be getting corrupted somehow? are you running Xposed or any other mod that may have created issues? Did you set the file permissions properly after replacing the files with stock?