Yes, the 3M seam sealer is very good to use. It has a strong solvent odor when you use it, so use a lot of ventilation so you don't breathe too much of it. The odor goes away after it dries a couple days.
I suggest cleaning your new metal with some acid metal prep solution first following the instructions. Or if you don't want to do that, you can clean the metal with some lacquer thinner and scuff it up with some 180 grit. After preparing the metal, go ahead and paint it on both sides with some black epoxy primer. Epoxy primer protects against rust very well all by itself. For more protection against rust, you can spray it with some good paint. After it dries a day, you can install the metal.
I would not use the bed liner spray. Not only do I not like the bed liner inside a car, but if you go back later to weld the pans down, the bed liner is in the way and have to be removed where ever you need to weld. Instead, lay some floor insulation down on your floors, which is how it was done originally. Some of the Pontiac restoration parts places sell pre-cut floor insulation, ready to lay in. Here's an interesting information page about original floor insulation:
http://www.firebirdtransamparts.com/techinfo/bingo/options/quiet/quiet.htm
