Problem after replaced the alternator on 1997 MB S320 W140

Today, the alternator died during driving and the battery drained out and stalled.

After installed new alternator, started the car.... The idle is little jumping and cause engine shaking for about 2 mins...then back to normal.

Before the alternator died, the car is no that problem.

Also, the windows automatic close function not working now too!

Anyone know why cause this?

I think that it may be the ECU got wrong information during the alternator fault. Is it the ECU will automatic reset by itself?

Hope anyone can get me some idea. Thanks