Thought it must be E450 since you mentioned Rear Pads and Rotors. The E350 didn't get rear disc till a few years later.
To navegator's point about ABS - I've done a goodly amount of brake work on our 2002 E450 chassis but have NOT replaced the Master Cylinder. Only Calipers and Hoses. I was able to flush and bleed the system by siphoning the Reservoir to Empty but NOT the chambers and didn't step on the brake till the Reservoir was full of new fluid. Then I bled the calipers, being careful to never let the Reservoir go dry and put air into the chambers. I this kept the ABS unit "wet" through the process. My understanding is that it requires a special scanner to analyze the ABS, and even to bleed the system if it gets air in it.
The possibility of binding brake pedal pivot or linkage is real. I haven't seen it since an old Dodge we had, but doesn't mean it can't happen. IF IF IF the pedal doesn't return to fully released position, then those little pointed ports won't be open to the Reservoir to let the pressure escape and brakes will remain applied.
