1st always weld a brace the opening before cutting anything out/off ,make sure the cab has been squared and level on whatever stands hold it off the ground and that they (the stands) are not holding the cab up by the floor pan only .4 jack stands and 2-2x6 boards can be used for lack of steel supports , I use a specific built wheeled stand for this stage with adjustable struts to maintain square .I need more pictures to see exactly what your having problems with but I would refrain from cutting so much out at one time and your floor braces just might be welded in the wrong position/height and that may be whats throwing you off and making the door hit ? measure 3 times cut and weld once !