For the cover bolts, like was said above, drill the heads off.
Have you tried this??
Use small screw drivers, awl etc and try picking out the screw heads so the screw driver can get down in them you may need a torch to see in there. Get a thru shaft screwdriver the right size, with it in the screw head propperly, smack it in with a hammer. Youd need it over an anvil of some sort, vice or something mounted in the vice. Clean the screw head out again. Then with a pin punch (bigger diamter than the head of the screw) give it a good hit or two. Clean again. Then again with the screw driver, hit it, the idea is to have the head cleaned out and give the screw driver something to seat in solidly. Also shock can help loosen the bolt. Then try and screw it out.
A couple of tips on drilling the heads off.
Get all nasty down in there with a centre punch and phillips head screwdriver etc to get rid of as much rust as you can. That rust dust is like grinding paste on the end of the drill bit and will make it blunt.
Drill gently as soon as the drill has the head removed off the bolt it will go all phsyco and rip half the plastic out of the cover down in the bottom of the hole.
You need a sharp drill bit, if its blunt you make heat and melt the plastic.
Like was said with ezi out and drilling etc. Ive only got a 1/4 unc tap so i use that. Ive used 1/4unc bolts too, its close enough. Bunnings have small blister packs with stainless 1/4 bolts in them. Got some here, if im keeping it i use them.
The other type cover, the one that slopes up from the front, you can just use the same bolts as what holds that tin cover to the engine. They are not down in holes so they tend not to rust as bad.
You can also flip the cover over and grind down flat then centre punch and drill whats left of the bolt out.
