1) WHY did you change the VCG & WHAT (a) performance issues & (b) Fault Codes did you have BEFORE you changed the VCG?
1a) Was there any OIL in any of the spark plug wells before or after you changed the VCG?
1b) Did you change ANY of the hoses attached to the intake manifold, particularly the hose that attaches to the rear of the VC when you changed the Valve Cover Gasket?
2) HOW did you check for vacuum leak (specifics)?
3) At WHAT engine temp, or after running for how long, does the engine stall at idle?
4) HOW (what tests used) did you determine the engine "runs lean all the time"?
5) If you clear the codes and drive the vehicle, what codes return in the first 5 minutes, and what is the Freeze Frame Data for each?
6) WHAT Scan Tool or Software do you have available for reading Fault Codes, Freeze Frame Data & Parameters?
With vacuum hoses that are 12 to 13 years old, it is quite likely that removing and replacing the Valve Cover will result in a cracked hose/ fitting and a vacuum leak. Any air leak into a hose connected to the Intake Manifold admits air which is "UN-metered" by the MAF, so the MAF is telling the DME to fuel for LESS air than is actually entering the engine, hence Lean Fueling.
As for the misfire codes, if ALL THREE Bank 2 cylinders are misfiring, what those 3 coils have in common is the SAME Ground point (X6177) per this TIS Installation Location:
I would suggest providing answers to the questions above, and doing further proper diagnostics BEFORE doing anything else.