Padjo, when you say your passenger door is off a bit, do you mean that it has actually moved from what might have been perfect alignment before or is it correctly aligned with the rest of the car and you are still getting water in? Sounds like the water is coming in from the window area. Door alignment is indeed trial and error, being careful not to set it off too much that it will kink the front fender (wing). The windows are indeed adjustable by taking the upholstered panels off and resetting the different bolts. Then too the windshield has a small amount of adjustment. The top (hood) frame also can be adjusted. There are additional rubber moldings available from TRF that will seal the window at the windshield against leakage. But these are all things that would be done on a complete rebuild and not a car that has been in use. Unless you have gone through some really torrential rains lately. Then, too, all Triumphs leak. Have you checked that the water isn't coming in from the firewall or scuttle areas? Good luck.
Bill