EE panels
Those things are like big stickers. I have a set (but not from EE) that I might be putting on my explorer. I painted it and was going to use the panels to help disguise any of my body work that could be seen. Not sure I if am going to use them now cause my work was pretty clean.
Anyway they are 4 1/2" wide pieces that have adheasive on the back of them. they are a PVC of somesort, so it is thicker than a regular sticker but not excessively. They pretty much stick on wherever you want them in that general location.
I had holes in my front fenders from the same molding i think you took off. I welded them up and would recommend that as the way to go.
It is really a pretty easy job. Pending you have a welder or a freind with one.
TIP: don't mess with trying to get a piece of metal in the hole. Get a piece of copper behind it as backing (go in through the wheel well) and you can fill the hole with weld. When you are done just pull the copper out. The weld won't stick to it since it distributes the heat so fast. Grind flush with the fender and use a little filler on top to make it smooth as can be.
Use the evercoat stuff if you can get your hands on it instead of bondo. It is just a finer filler and gives you better finished results.
Paint would be your big obsticle here. You can either rattle can the area and have it not look to great or paint the whole fender. if you are 2-tone you may be able to just mask at the line and respray the bottoms. Alot of guys use herc down there too.
If you want to try the panels shoot me a PM and I might be able to sell you the ones I have, cheaper than EE has them for, if i end up not using them