Hey Danny,
No model X5 diesel was fitted with swirl flaps. I went through exactly what you are doing now, when I got my '05 3.0d about 8 months ago (worrying).
The trans. reset is a good idea if you have changed any parts in the trans, had the trans open (fluid change) or are a new owner, with a different driving style than POs. Having said that, I'm a real supporter of the "if ain't broke..." philosophy. Regular maintenance aside of course. If the trans is good, maybe don't screw with it. I have read of adaptation resets going bad...
I did the same as you when I got mine - full service 2 with all BMW parts (at a BMW dealer - I have a mechanical warranty that requires this). Not sure if I'm going to take it back though - I wasn't all that happy with aspects of what they did. They did the trans. fluid check and adaptation reset though (at my request), which I'm very happy about.
Had to change the left front outer CV boot too - Spooky... Mind you, mine had 170,000km when I got it. 186,000km now. But it's in great nick.
Nothing else to major to do. Got a couple of rows of pixels on the MID that are a bit flaky - going at the moment but some days they drop out. Got some broken mesh in the front bumper (birdstrike) - I have some black alloy expanded mesh to fix that but waiting for a better reason to remove the front bumper (the clips are $$!).
Thinking I'll replace the front control arm bushes soon - have a WoF due in a couple of months and I'm sure they'll fail as the they are torn a little and I'm starting to get the front-end thud on sudden braking. Just need to find a 2-ton press!
But it's still the best vehicle I've ever driven/owned. Converted...