An un-restored 40 without rust at the bottom of the window frame does not exist unless it has been used exclusively in a dry desert. Fortunately, it is fairly easy to repair, and it is not the most visible part of the car as long as the window is up.
The most important thing is to avoid the frame from warping when you weld in new steel. For that reason, I split the welding job and cut out the rust in three rounds. And when I welded in again, I clamped the frame to a square tube. As always when welding sheet metal, it is important to proceed carefully and cool down all the time so it does not warp. See Welding sheet metal.
The overlapping joint at the bottom is always completely rusted. But instead of trying to make a new overlap, I cut out the overlapping steel so that the rounding of the outer steel was left, with a small upwards edge. Then I spot welded in the new parts, and used seam sealer to mimic an overlap. I am using 3M 08694. To get a smooth surface dip your finger in silicone remover or thinner first.
Before the new steel was welded in, I sandblasted the inside as best I could, and painted with epoxy. Where the spot welds would come, I used small pieces of tape to have blank steel and weld against, and then welding primer before welding.
After painting, I sprayed Fluid film inside the entire frame. This will prevent the remaining rust from developing further. See Painting and rust protection on rust treatment and Fluid Film.
More Landcruiser 40 topics here: land-cruiser-40
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