The kick panels really don't need to be screwed in. They fit very right once the carpet is installed and the back edge of the KP wraps around the metal edge adjacent to the door. If you need to add a screw just drill a new hole through the KP and the side wall. I think on most interiors there is just a single screw anyway.
The sill plates are a little trickier but I have done several installs and the holes in the sill plates match up amazingly well with the holes in the rocker panel. Get yourself an awl and use that to find the hole with the sill plate in place. The holes along the side of the sill plate and overlap the carpet are actually oblong and not round so that makes finding and hitting them easier. One trick is to make sure the two pieces of the carpet - that meet under the front seat - do not overlap under the sill plate. This is make an unsightly bulge and also make putting the screws in harder. Easiest to start by partially screwing in the screws on the top edge of the sill plate because the holes are nice and visible. Then press down and use the awl to locate the holes for the side screws. Some screws, especially those on the two ends - may go in at a slight angle.
Not sure where you picked up your door sill plates. Most Mustang Supply houses sell a "OE Ford tooling" plate and a less expensive "repro" plate. The OE plate usually fits and lines up perfectly. If you purchased the "repro" plate, that might be your problem.
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