So, Some little additions for anyone in the future who might be going through the same thing as me (2 months on into our fight with Aeroflot after they made us pay for rebooking flights)

- Aeroflot will try to fob you off with a incorrect Minimum connect time. (MCT) - which is from terminal to terminal. This is factually wrong - they should use the MCT between flights. You can find it here on the sheremetyevo website under "connections". Put in your flight details, and if possible - take a screenshot of it on the day, as sheremetyevo only shows 'today / tomorrow'
- (By the way: Aeroflot does sell tickets with connections that are less than the MCT. Our ticket had 1hr30 connection time. MCT was 1hr35. And Aeroflot strictly closes their gates 20 minutes early, which means we needed 1hr55)

- Flights regularly push off from the gate at Sheremetyevo early. Our intended flight pushed off 15 minutes before scheduled departure - and Aeroflot still had the greed to say it was 'our fault' for missing the flight and making us pay to rebook flights. If you miss your flight at Sheremetyevo - go to the flightaware website, and look up your departing flight - its one of the few websites that actually allow you to check if a flight has left early. You should have a much stronger case for missed connections if it has... (I was looking at some of the sheremetyevo departure flights on the flightaware website - about 20% of them were leaving the gate over 10 minutes early... I guess more rebooking fees for Aeroflot, so its worth their greedy while...)


-Finally, I guess the most important learning point (for us at least) is not to fly aeroflot. (prevention is better than cure!)