I did not have my Doors in, but I did have my Door openings braced. You know, I never had the thought that you have of bending the edge over, so I made some spacers and cut some strips to follow the countour, and boxed the flange (I didn't like the unfinished look of the flange either). You idea would work well too, I believe.
I used weld-thru Primer (I can't remember which brand, but don't use SEM! :nono: )-after I had it all welded in, I used Thinner and removed every bit of exposed weld-thru Primer I could, then I Epoxied inside and out. Remember, you don't need to slather on the weld-thru Primer, a good single coat will do.
As for filling the top, I think I would do the Firewall first (I did)-I filled my Top after I chopped it. I wish now that I would have bolted the tunnel to the Floor (for better access) but I was gung-ho at the time to have the Floor sealed as much as possible (for noise and fumes)-I think either way will work, I just know that with my engine combo that I am trying to keep the heat and noise out-I Seam sealed inside and out.
As for prepping the Firewall area for the weld, I used a Rolocs to get the major rust out of the inside flange of the Body, then a rotary wire brush on an air grinder (be careful!), then roloc scotchbrite discs (like these) http://freemansupply.com/3MRolocScotchBrite.htm
Then I cleaned the area with waterborne Wax & Grease remover and primed-overkill? Maybe-
The thing that I would change if I did it over again was that I used a spot weld cutter to get the old Firewall out, and while that works, it will swiss cheese your flange (had lots of spot welds)-use a small drill, like a 1/4" or so (just enough to break the weld), then use a panel knife (or substitute) like this- http://www.eastwood.com/panel-separating-knife.html
to separate the Firewall from the Body-I spent a lot of time getting the flange back where I wanted it and welding/grinding it.
Thanks for the compliment on the Tubs-it was a learning experience, but I needed them because of the narrowed rear axle-
I used the rear Bumper brackets to give the Body another place to mount, as I am not using Bumpers-the Wheels are 17X7 in the front and 20X10 in the rear-gotta love them Americans! I wish I lived closer, I would be happy to give you a hand-give me a shout if I can help more- :thumbup: