You should paint the flares the body color and put them back on, then loose the moldings. Those lines your talking about that were left behind from the flares, check to see if it wore through the clear and into the color, hopefully not past the color. Use a finger nail and see if you can feel that line, see if your nail drops into the line like a scratch or bumps over it. If your nail drops into you wont be able to completely get rid of it, it'll be too deep. If that's the case get some touch up paint in a pen form and fill the scratch with paint. Obviously clean the surface with a prepaint prep or alcohol. Give it a light wet sanding with 2500 to 3000 to flatten it out, then buff it back to shiney with a little compound and wax. If your pretty skilled with wet sanding you can obviously go with a lower grit to start to speed things up. I just recommend 25-3000 for the safety factory of taking too much off. If the line ends up being a bump, try to remove it with some adhesive remover or something, If that doesn't work give it a good compounding with a strong to mild compound and a rotary, if that doesn't take it off wet sanding will. Just use high grit and lots of soapy water and you'll be good. Your water should turn a milky color, if it starts to get dark you went too far and your in the color. You will however get a little darkness when wet sanding over any touch up paint you put down being it doesn't have clear over it.
