Here's a bit of info about the rust in the A-pillar door jamb. I just did a bunch of bodywork and rust repair on my 87 4Runner, here's what I learned. The rust that develops here is not because of a leaky sunroof drain. I thought the same thing before diving into my truck but I did a bit of surgery in the junkyard to a Pickup with the same rust and no sunroof. The rain gutter is spot welded to the inside of the A-pillar and then seam-sealed. The seam sealer cracks and lets water in between the rain gutter and the a-pillar. Here's a picture dump from me examining a junkyard truck (white) and working on my 4Runner (gray).
Here's the rain gutter peeled back a bit on the junkyard truck. As you can see, there is rust all along the entire length of the inside of the rain gutter. None of this was visible before peeling the rain gutter off.
Down at the bottom was the only rust that was visible before disassembly.
Up at the top you can see where the roof skin is brazed to the A-pillar.
Here's my truck after removing the rain gutter. You can see how bad the metal was pitted. One spot was eaten all the way through.
Here is the pillar with the spot welds ground down and the metal wire brushed.
And my solution. Pits all filled in and sanded smoothed.
Primed.
And painted.
Obviously this is a bit involved if you're not planning to repaint the truck, I just wanted to show what you can expect. My solution was to simply remove the front part of the rain gutter and fix the damage that had occurred so far. If you just want to buy some time, I'd say remove the cracked seam sealer and visible rust as much as possible, and re-apply new seam sealer. This will probably buy you years of time before it creeps back. It's not permanent but if you just want to keep your truck looking decent and dramatically slow the rust, this is a perfect solution. For color matched paint, you can try to find something close at your auto parts store, or for about $25 a can + shipping AutomotiveTouchup.com can send you rattle cans of color matched paint. I used them for my door jambs and I'm very pleased with the results. It sprays nice and even, matches good, and seems to be durable so far.
