i would get a good quality black roof repair mastic and apply it where ever you think water is getting in. sounds like it running inside the rubber seal and working its way into the car. also check the door frame is a tight fit around the door or you may need to pull the top of the door (tweak) the door in as
i got a thatcham on my car but no paperwork to prove it so the insurance wont list it as a thatcham alarm so you mayneed a not of teacher to prove you have a thatcham alarm fitted but we all know insurance companys already know
You don't bleed it by opening the 'drain pipe'(?). You remove the expansion tank cap and run it up to temp from cold at idle speed. Once the thermostat has opened you can refit the cap.
Thermostats can stick. it does sound like an air lock or partly blocked rad ?
Is the expansion tank cap okay? Is there a seal inside it? A faulty cap could cause the problem too.
If everything checks out okay it may be the pump is partly damaged and just not circulating the coolant fast enough - impeller loose on shaft, or broken blades on the impeller.
Sounds like the wires between the body and door has broken. Cut the rubber shielding and have a good look at the wires. Quite common thing to go. If you open the door and open window squeeze or wiggle the wires between door and body and you may find window will work when you move the wires. I doubt very much that it is the motor or switches .
metal can wear down even against a rubber seal especially if a little grit or metal deposits get in between the seal and shaft as already been said by stef.
the seal should be a nice tight fit on the shaft. when you slide the seal on the shaft it should be tight then as it get to where it sits does it get easier to get in place ie the last couple of mil is looser than when first putting it onto the shaft if thats the case its the shaft that wore down i recon.
remove plugs and fit new. they will come out even if cold. if they dont make any diffrence replace the ht leads as they fail. as it was run to empty i would change the fuel filter as it most prob needs doing. its located under the car near the rear nearsid wheel. it looks like a soft drinks can