How do you get to this seam if you pull the fender off?
I have been fighting this same battle!! The first time I accessed the inside of the cowl I took both fenders off and cut out the subframe section that covers the cowl channel (metal surrounding the approx 2" drain hole) cleaned the area up and welded in patch panels of sheet metal then tared the crap out of it.
Once finished inside the cowl channel I welded the cut out pieces back in place.
I still have leaking problems though!!! I believe that I didin't do a good enough job sealing the holes (I used a cheap handy core buzz box for the welding with not much experience).
Interesting idea of using bedliner to seal up the channel, I have heard of pouring liberal amounts of cleaner as a prep(paint thinner, acetone etc..) and then using marine grade fiberglass epoxy resin poured into the access panels on top of the cowl in coats.
My rust is really bad in there though, and has gone right through the seam where the firewall, wheel well , and cowl channel meet. Its the area under the hood that is right below the windsheild wiper motor assembly on the passenger side and under the clutch/brake booster on the drivers side. I have also welded in patch panels there!
A toyota tech that I know has an 89 4runner (gen 1) and he accessed the cowl channel by removing the wiper motor assembly, the hood, and hinges. This wont work on my 89 p/u because I have a different hinge and wiper configuration with the newer body style!
I have considered plugging the cowl channel access vents on top to prevent water from entering but I am currently debating it's implications as to where the water will go and I will be sucking air for the cabin from the side access ports under side fender instead of fresh air on top.
Also its good to mention that since I have leaking water pooling in the footwell areas I have relocated my engine computer into the glove box to keep it dry (see 4crawler's site for how to in the cheap tricks section). I just wonder how much of my wiring is corroding!! My circuit opening relay bit the dust last winter from rust as well.
About the leaking windsheild thing I removed the interior plastic A pillar covers on the sides of the windsheild and all looks good, I am still planning to remove the dash for a better look but have not had the time because this is my DD!
Oh well sorry about the Long post but it is nice to hear other people have this problem as well, I am just trying to share my experiences/frustration so far.
Please if anybody has and other useful info please fill us in... so we can fill our holes with something good ( and solve this problem!!!).