If it was me, I would get a DA sander with some 150 grit and sand the areas with it to smooth out the grinding scratches. if they left any paint in these areas you will need to feather the paint edge also so it wont leave an edge .
Omni makes a quality primer in its product line i think,(been awhile since i even used it) stay with all compatiable products, dont mix brands when it comes to primer, paint & clear!!!!!
Prime area with 3-4 coats of primer , let sit for 24 hours. wet block with 400 grit , wipe dry, seal & paint .
Your areas that you are doing the glass work at might want to prime then, block sand dry with 220 grit, then reprime , wet sand 400 , then seal and paint.

SprayTech