The transmission issue is not good. You might have damaged the front pump when installing the new torque converter or it could be a problem with the oil pick up on the filter but either way you had a problem before so maybe looking at some serious trans work.
The double speed thing is interesting, it could be a problem with both rise AND fall of the signal being counted instead of just rise OR fall.
The headlights are different for facelift and will require a different LCM or at least different programming so that might explain the headlights.
I didn't know the 3.0L even was available with air suspension?

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1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)