The back-hang side rails should be lower (2-3") than the elevation at front header to keep the door from closing when not hooked to an opener (springs/torsion bar alone). This is a safety feature installers are taught when installing doors (for use without openers). Four inches sounds excessive, check on-line with the door manufacturers directions. The new bent center arm should work with the opener, just don't reverse it (the bend end).
Gary
Gary