I've had a look at diagram, well done. From that it looks as though the pump is pumping straight over through vent, each time this happens air will be sucked in causing sludge to accumulate. I must add when flushing an open vented system the cold feed and vent should be blanked off. You say the pump was making an unnatural sound, a pump when spinning acts as a magnet, drawing in and accumulating the magnetic sludge, I suspect this is clogged up, working enough to pump over through a path of minimal resistance but not enough to get heat to up stairs rads which could offer a lot of resistance or further blockages. Sludge to start off with will gather at bottom of rads, further building up over time. You could stick a strong magnet against the flow and return of upstairs rads to see if there is sludge there, remember copper cant be magnetized but steel obviously is, so put magnet against copper pipes, if it sticks you know theres a large build up of sludge. I once had a system with 22mm pipe having an internal bore of 2 or 3mm the sludge was that bad, piped similar to this picture.
Personally I would recommend the whole system be reconfigured to prevent this venting over and properly power flushed. Sealed system will do away with the worry of venting over and allow positioning of the pump where it is, it needs to be fully pumped, complete thermostatic control with independent zones. As it stands, from what your diagram says matters wont improve