Does this work for the side covers? Or will I end up with a smoking puddle of goo? Also good for the frame? As I want to repaint the frame also.
Any will work but the good stuff takes less time and the frame is liable to be heavily coated.
use it on the side covers as it will eat right through the plastic. I repeat DO NOT!
For the sides just lightly wet sand using 320 followed by 400, then a light coat of primer.
Fill in any obvious nicks with glazing putty and give it days to dry or use common Bondo but in either case be sure you've sanded into the nicked area(s) Bondo will set up in fairly short order but glazing putty takes a bit of time until it fully cures.
Look at them under all sorts of light levels and when you're sure they're perfect then you can use a primer/sealer such as http://www.duplicolor.com/products/primerSealer/
if you got the sanding done right, if not get a sandable primer and start with that then touch it up with 400 or even all the way to 2000 paper in the sink with plenty of water.
What kind of perfection are you looking for and what kind of paint are you using?