Hopefully you've got it all addressed.
If the passenger door wasn't closing properly, it would not have automatically locked. That could cause a number of your problems.
(I had a VW Passat that had a "hood open" sensor that broke shortly after I bought it; and it stopped beeping when locked.)
Just a note:
The A01 service warning indicates "soon" at around 6000 miles, but doesn't say "Due Now" until around 7500 miles. (And then it starts counting up how many days you are late. I did my service around 3 days late.)
So don't rush in at 6000 miles; wait for "due now". (Which is...