Haven't rewatched, but the Dr says 'follow Nasreen to the tardis' - which makes sense because she knows where it is. But then she doesn't go - so how do they know where the Tardis is?

It would have been easy enough not to mention 'follow Nasreen', and then it would be simple to ignore that no one knows where they are going - so is this a clue?

Given that the director somehow seriously managed to get part one to overrun by 15 mins, chances are part 2 overran also and they had to cut some of the less improtant scenes, especially the running down corridors variety?

At one point, they were all running down the corridors then they stopped and waited for the Doctor as if they were unsure. He came along shouting something like "what are you waiting for" and ran past and took the lead.

Was it my imagination or was there one scene where MS didn't have his hands tied, then in the next one, they were?

Yep: Check out iPlayer @11:32s and 11:53s!

K