I've not done anything to the upper except cleco it in but have been wondering how I get that to lay flat where it's not.
Because of the radius of the fairing, the usual spots to screw to don't actually touch at the rivet lines. So I may have to go outboard and attach to the forward and rear spar rivet spots instead. Right now that's only 3 attach points but I'd like to get a few more if I can. Possibly the clickbond in the skin will be needed.
Remove any high spots on the underside of the pre-made upper fairing, just as Bill said. When well fitted, close any remaining edge gaps to zero with a liquid shim. Roughen the underside of the flanges with 80 grit. Tape the metal surfaces with a neat strip of packing tape. Mix epoxy with cabosil to the consistency of toothpaste. Apply a bead along the underside of the fairing flanges, screw it to the airframe, and allow it to cure. After cure, sand the edges to their final contour, a nice half-round.
Look close at the edge where the fairing meets the horizontal stabilizer. See the narrow band of cured shim material?
A similar dot of liquid shim can be used to make a solid base under each screw location, so tightening the screw doesn't deform the surface.
Your new scratch-built lower fairing is a nice part...my compliments. Bill E's proseal glue-on suggestion is a good one. Mine is attached with three screws per side, tapped into the longeron. Whatever works.
I know most upper fairings are attached with a whole lot of screws through the VS and HS skins, but it's not really necessary. Build a "hook" at the leading edge, and it locks into place using just two screws in shear, one on each side. At the rear, I use just two screws per side.
I like the screwless look. Be aware that no long fairing will fit
perfectly at all temperatures; epoxy glass has a CTE about 2/3 that of aluminum.