Shuddering start after service done on Upper Timing Gasket leak / Alternator failure

[jpn42]

Hi, I'm new to this forum but have been on Bimmerfest since buying this car in November.

The alternator failed in my X5 due to an oil leak from the upper timing cover gasket on that side. I took it to an indy and he replaced the alternator, belts, the timing chain gaskets (both sides), valve cover seals (both sides), Camshaft Solenoid gaskets, Eccentric Shaft Sensor, Position Sensor O ring, spark plugs, and spark plug tube seals.

There is something that has cropped up right after all of that work was done that wasn't happening before I took it in. The tech is perplexed, as am I.
When he reset all of the codes after doing the alternator/ valve cover work and then started the X5 it starts very roughly and slowly settles down. It feels the same as the moment the alternator had died and the transfail safe warning came on (my original issue). The Service Engine Soon light is on now but no other warning lights.
When the tech was testing the issue he said that it threw a misfire in Bank2 code. But he doesn't know why as everything was just taken apart and put back together (new spark plugs as well).
The sputters stop after about a minute of idle and only the first acceleration from parked is rough. It's pretty smooth and gets even smoother from then on until the next park and off.

I was able to get the codes that are being thrown after all of the work that's been done so far. The strange thing to me is that the sputtering rough start and first acceleration wasn't happening at all before the alternator failure on the 4th (my original problem).

Here are the codes I was given:
Before the work:
2EFE Fan (Tech explained that he'd forgotten to do something before trying to start the car)
2A89 Exhaust Vanos 2
29CC Combustion Misfire Several Cylinders
29D4 Combustion Misfire Cyl 8
29D2 Combustion Misfire Cyl 6
2A84 Inlet Vanos 2

Codes Remaining after Alternator and seals work:
2A89 Exhaust Vanos 2
2A84 Inlet Vanos 2
And the Service Engine Soon light is on.

As I mentioned before, they are perplexed. Could anyone shed some light on what this might be, given the work that's been done so far?

Thanks for your help.

2006 X5 4.4i 103k miles