EGR's were the original big problem with MK7's .. there have been a couple of revisions since, one with metal rather than plastic gears
& then a water cooled metal geared one..
Still giving loads of problems but , (purely from what i see here ) fuel pr4essure control issues are the main problem these days..
The MAP sensors still work gunked up but work better / run better clean.. just clean out the sensor with a paint brush & WD40 every so often..
With the EGR deleted they wont gunk up half as much...
Yours sound like whatever s causing the problem hasn't been fixed yet, sorry to state the obvious
With all that PCM update stuff already carried out on yours , I'd unplug the EGR & see if any symptoms change, or if you can get the fault codes read, & any are EGR/MAF related like below, blank the EGR's feed & test again..
P0404 - General EGR code
P0401/2/3, too much . too little EGR etc
P1103/4 MAF sensor reading to high or too low , this indicates a faulty EGR not a faulty MAF sensor. Its the MAF sensor sitting upstream effectively monitoring the EGR that results in the 1103/2 codes, most of the time..