When I did it, I put the EGR pipe and connectors back and then the pipe with all the various connectors. Make sure to carefully cleaning the DEF injector. I may have some buildup on the tip. I just used water to soften it. After returning to stock on the MM, I had a DEF fault that triggered the 50 miles till 50 mph then it went to idle only mode after about 10 miles. I was able to drive to the dealer with the off tune and then return to stock before they hooked up the IDS. They will likely have to erase the ECM and then reflash with the latest calibration. I also topped off the DEF tank at the same time. Just last week after 6 months of running on-tunes on the EZ-Lynk, I got a NOx sensor code and then a DEF quality code. Same deal, back to the dealer. The latest strategy is smooth on my truck. I'm told the EZ-lynk tuning software coming out soon will have the option to build a tune with a current FORD calibration specific to your build and not the old universal crap from 2010-11 when the calibrations were disassembled. AKA the 2013 trans solenoid buzz when the TCM is tuned.
If you're wondering, I put it back to stock because of some weird tuning issues, cold start white smoke, low boost codes after heavy towing and it's nice without the exhaust smell. I only lost about 1 mpg. Towing mileage is the same.
