re: Add the final leg of my Europe trip.

When you say the flights aren't lining up for Krakow, what do you mean? I see one very cheap option that leaves Krakow Sunday night with a 13 hour layover in Zurich so you'd essentially get back on Monday the 17th instead of Sunday. Another option is returning from Katowice (KTW), they have flights leaving that Sunday morning and you'd be home by Sunday night. Google flights for Barcelona/Katowice Poland

How about returning from Copenhagen or Berlin? Copenhagen is at $738, Berlin I think is $771.

I went to both of these places in February and had a great time. Copenhagen takes about 3 days to see/experience everything so that sounds like the perfect amount of time. Berlin is great if you are into history/WW2 type of stuff. Since you're already going to Munich though, I'd probably stick with another country just to see what each place has to offer.