I agree Eric, since you went base clear you will take a hit concerning OE, but only a minor one. Go ahead and shine it up. HOWEVER, I'd highly reccomend a proper OE style grey sealer/primer with color over spray from the sides on the underside just like you have now. The fully painted undercarriage is a dated (and incorrect) look from back in the days that many people just didn't know any better. If you ever decide to sell the car I can gaurantee you that it will drive away a good many potential buyers.

*On the frame....Grind it, fill it, smooth it, carefully fog on some red paint to cover the work