Thanks for the replies so far. Pics incoming but to answer your questions:
the purlin sockets do seem to line up with the edge of the stack. the chimney breasts is within the thickness of the party wall.
I haven't had the roof re-done, but there is a breathable membrane indicating it has been done in modern times.
When I bought the house there was signs of leaking in the same spot, which is why I did all the work I've done so far, thinking it would rectify it.
I did notice, since the flashing and leadwork, the leak appeared worse than before. it was a trickle before, now it's more like a steady stream.
Flaunchings were re-done when I had a wood burner fitted as it needed lining and a new pot fitting.