My main tip for avoiding leaks is to put a 'shower cap' on the car. I've used normal sheets, plastic wrap etc.
The main areas water comes into mine (original roof with ash bar at front) is around the point where the windows meet the roof and the rubber trim at the front by the a pillar.
covering this aea with a sheet is pretty effective. Certainly saved any wet inside whilst parked out in frankly tropical storm conditions in the south of france last summer..
On the move, I just ignore the odd drip, though I'm sure that maybe re-waterproofing the hood might help water roll off rather than soak through perhaps?
:-) can sort out both those issues... dad's Mk1 roof it fine and rareley needs to have the storm cover on. Sounds like this is sovlveable.. the water beeding on the roof can be sorted without additional waterproofing, just correct cleaning and conditioning. Dad had a similar problem on his 4/4 he uses daily.
As for your quarter light problems.. it depends on what series door inner you have, I expect you have similar to dad's. The general problem (on either) is that Morgan did not fit (but made suitable preparatory holes for) the lower window mechanism/frame bracing. Esentially over time the upper screws allow slight movement and the lower part of the mechanism ends up only bieng held straight by the inner door trim (however don't try to push the top of the "A" pillar back by hand as you won't move it).
In reality this is slightly more difficult than it sounds. :-)
