Gearhead, I like what you've done. I have a scratch in the lower area of one of my bags, that starts below the bottom-most "rib" and runs through the area that's already texturized. So in my case, just coating the top third wouldn't help. I'm seriously considering entirely coating both bags.
Anyway, I don't know anything about wet sanding. I wonder if you could give a little more detail about what sandpaper you used and how you did the sanding? Did you do all the sanding with 400 grit, or did you start out with something more coarse and finish with 400 grit? Was it just your basic 400 grit paper that I'd buy at any hardware store, or do you need some special type of sandpaper to wet-sand plastic? Did you do the sanding by hand, or did you use a machine?
I'm not an expert at sanding and prepping by any means, but the basic idea is just to at least scuff up the clear coat a little so that the new paint (or bedliner) will stick. I think I did use some courser paper (maybe 150 or 220 grit) to try to sand out the scratch itself, but the bedliner will do a decent job of filling in the scratch if it's not too deep. You can get the wet/dry sand paper at any auto parts store. I think the main purpose of using it wet is to keep the paper from clogging up with dust. I just used a small bowl filled with water and added a couple drops of Dawn dish soap. Just dip the paper in there and keep it wet. Since you're applying a thick, textured material, you don't need to be too careful. More than likely you could just lightly sand it with some regular 220 grit paper, wash it well, and paint away. Also, I've since used the bedliner spray on a couple projects at home and work and I found that I like the Rustoleum brand better than the Dupli-Color brand. I think it's cheaper too, about $7/can at Home Depot. The stuff sprays out pretty heavy so I would recommend practicing on a piece of cardboard or something first so you know what to expect when spraying.