Wouldn't worry too much about the scratches. Primer will stick better with the surface roughed up. You can smooth out any scratches that might show after primered by sanding with about 220 grit paper. I'm not familiar with Prep All. If the label says it's to use before painting it should be. I know some stuff like tar remover that some use has kerosene in it and that will cause problems. I always used thinner/reducer to wipe down parts before painting but that was with PIG products. Be sure if you used any paint stripper to be sure you got it all off. That stuff will ruin a paint job fast...check around all places where brackets are welded to a part, etc. like around welded on mounting nuts on a bracket. I always sanded the part, wiped part down with thinner, then wiped with a tack rag to pick up any dust and then paint. Used a tack rag right before Jeffery coat if paint is allowed to dry between coats.
1980 LTD (changed over the years), 1979 LTD (being rebuilt), 1977 KZ turbo and various KZ's in various states of build. KLX110