Saving and Repairing Grazed Engine Covers.

On the proviso... you didn't gouge a hole right through your precious engine covers, you may just be in luck. 
After the Gixer took the fall, I was surprised to see the alternator cover was still oil tight. Yes, it was in a bit of a mess, worn down and scratched to buggery but, to be fair, it was already in need of a repaint before the accident as it was stone chipped and a bit dull. Definitely on the list of things to be done in no great urgency. Now it was a little more urgent.

New covers or secondhand?
My initial thought was just get a new one, then scour eBay for a nice used example, but then I wondered if it would clean up enough for painting. Not much to lose really. It wasn't leaking and, being low down, wasn't exactly in your line of vision. It's surprising what you can get away with in bodywork just by "taking your eye off it".
So it was out with the 80 grit emery cloth and a block. It doesn't take long to run down aluminium, and within 15mins was looking a hell of a lot smoother. Block the larger, flat areas, then use your hands to keep the corners smooth and keep the original curves of the casting. The lower part of the cover is ground away, but I need that for better cornering clearance... honest.

All of the deep road rash scratches must be removed for a good, final finish. The 80 grit soon had it looking reasonable; then it was time for 180, 240 and finally the 320 grade wet & dry (used wet) to get the cover smooth enough for paint. Because the cover wasn't being removed, and there is still paint around the bolts, the paint must be feathered so you don't see a line once painted. Use the 320 grit to make a smooth transition from paint to bare metal. Any paint left on the cover must be "keyed" to allow the new paint to stick. A green scotch pad is ideal to take the sheen off it.

With aluminium dust everywhere, I pushed it outside to hose it down. Once in, I used the airline to dry that side and cleaned the cover and surrounding area with brake clean and a clean rag. Mask the heads of the bolts and the crankcases, working your way out before covering the side of the bike in newspaper.

I'm using the gloss black caliper paint again. Apply a very light dusting first to see if there's any reaction between the old paint. Happy to say this didn't happen! 

Without trying to teach granny to suck eggs, don't apply too much paint on each coat. Painting vertical surfaces is always harder because it's liable to run. I still find it difficult. When you have an engine cover mounted flat, on a table for instance, you can really lace it on there and get a cracking finish.

With concerns about getting it on there too wet, I did end up with a slight orange peel effect. I can live with that until I find another cover.

The extra clearance I'll get from this cover is just what I need for Marquez's 63° angles of lean. (Or I'll just stick to the 10° I normally hit.)

Important to remember!
Fix your cases like this and you risk putting a hole in them next time you hit the deck. It's easy enough to break through them in a crash anyway but, with the casting being this much thinner, might be the difference between riding it home or needing a tow truck. You pays your money and takes your choice.