Here is the part I dread the most: Sanding. Make sure to wear a respirator, safety glasses, and very old clothers. Work outside if possible. Use 60 grit sand paper with your power sander, and then 100 grit to get the fleece as smooth as possible. Worry only about imperfections that rise up, do not mess around with trying to get gouges or pits. Wash off the residue with a wet paper towel, and then mix up some body filler with hardener to being the finishing process. Using a spreader, push the body filler into all of the pits and imperfections. Some people cover their whole projects in body filler, although I concentrated on the problem areas (much less sanding). Make sure to get the filler as smooth as possible before it dries. After the filler dries, sand it down wit 100 grit, and then inspect. Chances are you will have to repeat the body filler phase several times. When everything looks good, fix any final imperfections with glazing putty. It works great when you wear latex gloves & spread it on with your fingers. Wash everything off with a wet paper towel. Note the beige patches in the picture are the areas where body filler was used.
Getting close to the end... Sand everything with 150 grit sandpaper, and finally 220. If you are going to paint your panels, then you will want to wetsand even higher, but that will not be covered in this How-To. When you are done sanding, wipe the panels off with another paper towel. Coat everything in a primer, and inspect for any final problems. If everything looks good, then you are set for the final finish.
Time to finish the panels. You have a variety of options, including paint, texure spray, vinyl, and carbon fiber. I first attempted a silver paint finish. It looked great, but it would not be very durable in a high traffic area like the door panels. Vinyl is a technique in which a material is streched over the panels and held in place (generally with staples or glue), and has a variety of OEM textures & colors. Carbon fiber could be applied much in the way you added fiberglass mat, only with one piece instead of many. Carbon fiber is expensive, and you have to be experienced with it to get a desirable finish.
I decided to go with a texture-spray finish. I used Duplicolor truck bed liner, and am very happy with the results. It has a rubbery finish, and is very durable. SEM also makes a texture spray that can be dyed to match your interior color, although if black or white works best for you, then a bed liner spray is probably the way to go. It is cheap and easy to use.
I always planned to go back and cover the panels in vinyl, but ended up buying the IS300 right around the time I would have done so. After around 72K on the car, I only resprayed the panels once, so the finish is very durable.