Although coincidences happen it would seem there is some link between the AT work and this problem. To take the AT out they would have taken down the exhaust and I would start looking there. The other issue is, they may have taken the top two bolts out from the top and disturbed something at the back iof the intake manifold.

Why not take it back to the guys who did the AT work?

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2003 4.4i black ext./black int./black headliner (kid's runabout)
2014 535d X-drive, M package, silver/black interior

Sold but not forgotten:
2009 E70 35d, black ext./black int./black headliner (sold 2021)
2006 4.8iS Le Mans blue/cream int./black headliner, SOLD in 2012 sadly...

Other hardware:
2015 Cayenne S (wife's new DD and definitely wroooommmmm)
2016 Tundra 1794 edition crew cab, luxo hauler
2005 Tundra crew cab, weekend hauler. Sold after 150k very happy miles.