Clear will cover up some relatively heavy scratches, depending on the viscosity of the clear of course.
I sanded my taillights with 400 grit on my DA and cleared directly over that.
It helps to do a blow-tacking prior to paint. After you panels are all wiped down and masked, using an airblower at low pressure begin at the highest point anywhere close to where you'll be painting and blow over the panels going smoothly downwards while using a clean tack rag in your other hand to wipe immediately behind the area you just have blown the dust off of. Do that all the way to the bottom of the panels. Then right before you get ready to spray, tack the panel without the blower one more time.
The second tacking picks up any dust that resettled onto the panel.
Guess I should have mentioned this to you when we talked, sorry Bill.
I always remove any masking from the prepping stage and remask prior to painting a vehicle. I also clean the living hell out of any place I'll stick tape too. Blow dust off, wipe it down, mask. Then wax and grease remove, blow tack, let it settle for a couple minutes, tack again and paint.
Pictures of the EB?
The cowel looks great btw.