do's and don'ts of clear coat touchups?

Besides that small spot where the paint lifted from the metal on the right quarter (will be under vinyl top trim) and a small nick the size of a pin I made when installing the front bumper, there's a couple spots I need to fix elsewhere, very small, but will take half a day, I'm sure.

I wondered.......... most of the areas are so small I'll probably use a fine artists brush, that other area where it lifted will be pretty well hidden, it's at the edge of the vinyl top, next to the drip rail, behind the quarter window. So trim will cover all if not most of it.
So just stick with the AE, which I already have, I suppose. My big thing is to prevent further damage, and since the one area is down to bare steel, I need to take special care there.

The only problem with BC is repairs! The only real choice is AE for small repairs. If it's a big one BC is all but impossible to get a good blend from new to old. I've always been told the only way is to paint the entire panel, or maybe from a hard body line (especially if there's a piece of chrome covering the edge) or some other visual separator to a panel edge or another seam/separator. Like on a 65-66 Classic you could remove the top edge chrome and repaint from the edge over to the hood, but would still have to paint the entire length of the fender -- just to repair a ding or deep scratch. Makes me wish I'd had my car done in AE or a single stage urethane rather than BC. Repairing a panel with the flames will be tough! 

Since the car was painted in BC/CC, I wouldn't patch with any other type of paint. It will be more visible.

Unless you're painting entire panels, keep the touchup area as small as possible. The larger it is, the more visible it will be.

For the pinhole marks, unless the knick is through the colour, just fill the hole with clear on the end of a toothpick or cut off Q-tip. It will be less visible if you use the same clear that was used on the rest of the car. Clears are all slightly tinted. Mixing different clears will show the repair. Add a touch of hardener, and the repair can be cut and polished to blend it in with the rest of the panel.

The larger area where the paint fell off was not prep'ed properly in the first place. Make sure you scuff up the area properly and clean it well with wax/grease remover. Make sure you get to all the areas under the vinyl where the paint has come off, otherwise you will get rust blisters under the vinyl. Again, keep the patch as small as possible. Use the eraser end of a pencil to drive the sandpaper. Apply the primer and colour with a small modeling brush. Lightly scuff the surrounding clear (not through to the colour), to blend in the new clear. Use an airbrush or similar to spray the clear (with hardener ), then buff it out when it is dry. Don't worry too much about overspraying the past the patch, when you buff it out, it will all clean up.

Use 400-600 grit paper to prep bare metal and primer. Wet sand the clear with 1000-1500-2000 grit before buffing out with your favourite compound. Work the patch area as little as possible.