I'm not a native speaker, but I'll try to answer your question because I've been learning English for some years.
So, 1) were doing - because the sentanse begins with "aren't you" - this is PRESENT SIMPLE, that's why the second part can't be used with PAST PERFECT CONTINUOUS.
2) has passed
3) I think two variants are possible. But I prefer more the first one (was sitting).
I think so!