Hi David, I spent weeks chasing the same leak. My observations were, the boot seal has air holes in it, so when you close the lid, it lets out air and prevents the lid bouncing, I sealed the hole nearest the leak.
Also, I had a rip in the window seal near the top, discovered water was getting in through the clip, down the window inside the boot lid, dripping down into the boot. Sealed with Captain Tolley's along the top, sealant underneath, and now, touch wood, all dry.
If MG/Rover made submarines eh