To determine the correct size holes, I use dial calipers on the tube/sleeve/barrel nuts. This measurement tells me the maximum and minimum sizes, the maximum measured over the tube nut "prongs", the minimum measured over the tube nut "prong" with one pin of the emblem installed. Then the hole is drilled. I usually use a smaller size to make a pilot hole, then drill the full size (if you don't do this regularly, a two step drilling is recommended). Occasionally a round "watch" file maybe be used, especially after painting. If the hole is there, select the determined drill size to use to measure the hole.
The "nuts" go in before the emblem. Make sure the "prongs" engage the backside of the hole.
Part numbers are:
GT emblems - 378362-S102 (3/32 pin)
Engine emblem - 37548-S102 (3/16 pin)
They are available from AMK in kits only.
See the appropriate Mustang Body Assembly Manual (either 65 or 66, you didn't say) for more information. Get an entire set. You can thank me later.
Jim