Are you getting any warning when you start the car like check coolant, just ive got a AGU as well and everything you have said seamed to be happen with mine, poor mpg, flat spots, mine also was cutting out when driving or stalling when sat.
Turns out mine was a fault temp sensor, changed it and im back up 8mpg, no more flat spots and cutting out while driving so im happy
You can check the maf, disconnect it and if there is no difference then it could be maf, If you can get checked with vag-com