Well I have to jump in and confront my rusted cowl. I have the outer, inner and the outer to inner panels already and have accessed what needs to be replace. I noticed that on the original inner cowl, there seems to be a piece that wraps around the firewall on the front, much like the outer cowl panel. I also did a search and checked out postings on this page. Sounds like no one cherishes the job, but taking time and checking for fit along the process is essential. Fortunately it looks like my inner to outer piece may not need to be replaced, it only has a little rust on the spot weld flange, and only the bottom area on the outer cowl panel. The inner is the worse of the pieces.
I also watched "Body Panel Replacement" by Kevin Tetz since I have never done this type of work before and found it quite helpful. I am just a bit nervous about cutting into my truck, but it isn't going to heal itself. I'll take pictures along the process and most definitely will be asking questions as I go. I have some photos of the rusted areas in my online albums.
http://share.shutterfly.com/share/received/welcome.sfly?fid=6e336436e6d9422c&sid=8Ibs2LFo3bs3MNothing ventured, nothing gained.