Did you use aftermarket door seals? If so how does the door shut line look from the outside?
If the seal material is too hard and does not easily compress it can force the window part of the door outwards giving poor shut lines and a leaky door.
Apparently this is one time when genuine LR parts are what you need.
Brittanica Restorations is basically a Yorkshire lad restoring LRs in Canada and making some interesting videos about it.

So far, most of the water must've been coming through this gap between my gear box tunnel and the seat box. I've sika flexed it up, but I thought at first that my tunnel had rotted away from the box, but it's still a bit strange to me? Then I was sat in the car and it was sunny. I can see the ground through the oval grommet. Then, one of the rawl plug typr rubber grommets that takes a screw to keep the handbrake flange on was not in situ. Yes, there are quite a few water inlets in a landy. I've not even looked around bulkhead seals etc. yet