I'm concerned meh boy pios, that you're cutting into the surface area of the light so much that you're actually reducing the output of each headlight. Have you tried out the lights with the lids on to see how much more dimmer the lights are?
To get rid of them holes, either use glazing putty or mix a few drops of fiberglass resin with the filler, use the normal filler creme hardener, plus a tad extra, and it will self level and run smooth. It dries real quick, so don't wait till its real hard to start sanding.
Wet sand the thing with 220 sand paper afterwards (water with a lil squeezy)
