So he will now proceed to "fix" the rest of the press to fit the altered shoe. His entire press will be exactly the distance, center to center, of the two holes, OFF everywhere else.
Okay, I was just having a little fun with you on this part. I have seen things in my life "fixed" like this though. I've seen a guy put the track on the bottom of a drawer backwards. The drawer was then 1/2" to far to the left, so he hogged out the hole in the dresser for the drawer.
There is a plastic gear in the shellplate that advances things. It is VERY easily damaged. Check that part out. One wrong move while setting the timing can wipe it out. So can reversing the shellplate at the wrong time. You don't need a pipe wrench to wreck it. Order a couple, they're cheap, and good to have around.
It sounds to me like your plate is not indexing properly. That gear might be wiped out, or it might need another quarter turn on the adjusting screw. The screw should be turned until the plate locks into position, and then turned a little bit more.
Also, look at the part Lee calls the "drive bolt". When he says to use finger pressure only to tighten, he really means it. It is so soft it feels like it's made out of lead. You can get into trouble with that thing while disassembling the shellplate. It's a reverse thread and if you forget, you will tighten it while trying tot take it off. Now it will be too tight and need pliers to remove, which WILL ruin it. Get a couple of those when you order the white plastic gear.
You didn't damage anything with your extra hole, and I don't think you moved the entire universe 0.25" to the left, but I bet when you get this all figured out, you won't need the "extra" hole.