As far as the engine
 

Well heres a little tidbit. I had a similar issue with the tapping on my E60 530xi and my SA told me it was normal operation.

I know the e60 has the N53 engine and our X's have a similar N52 engine. I have one of the last produced 08 X5's manufactured in 12/08 (I know I couldn't believe it either) so it stands that I have the N52 with the revised heads....until I started it the other day. Same engine stumble but smooths out after a couple seconds. I also noticed a slight shudder when cruising at highway speeds. My indy and I are going to do a plug change (its due). As far as the intake....everything is tight and true.

I had the rough idle problem that seemed to work itself out with a couple cycles of fuel injection cleaner, a filter and a few rounds of Shell Gas.

OP
Any resolution ever?

Using concetrated chevron with techron fuel injector cleaner should clear up any problems after two tankfuls of use. Just add right before fueling up and try not to add over 18 gallons of gas to the concentrate so it can still work out any residue in the injectors.