I took some better shots yesterday (because they didn't show up when I clicked on this thread..because they're on page two), and no, I haven't filled the holes yet..
I'm about to tackle a very similar situation on a (Paul) Newson I just got with Waverly tuners. The holes are drilled per Paul Hostetter's #3 diagram, I.E. the hole is the diameter (or slightly larger for a somewhat less-than-snug fit) of the collar (bushing). Waverly tuners don't like this, for some reason, so I'm going back to square one in hopes of getting the post gear to mesh properly with the worm gear. Several of them under tension are pulled apart, creating a full 90° of play. Tuning is a nightmare. Maybe if I replaced the tuners with a less 'engineered' Gotoh set, they would be more forgiving, and I could avoid surgery altogether?
I don't know if this was already discussed in the thread because I can't remember that far back but I want to point out that compared to my snakehead, your tuners are mounted on the wrong sides. The gear should be down so that the string tensions pulls the shaft gear into the worm gear. It may clear up your tuning issue if you switch the heads around so the gears are below the knob.
Snakeheads have worm-under machines. I think he did the right thing.
I had previously reamed out the original holes to fit the later post spacing required to accommodate the Schallers I was fitting to replace the originals. In my opinion, no gears in this 'modern' (from around late 1924) configuration of 'worm over gear' can
a) look right on a '20s snakehead, or
b) work right when reversed. They turn backwards.
They are also too heavy for the balance of the instrument. The new 'vintage replacement' are the almost perfect weight and almost perfect fit (- see the original wiggle end marks in the wood).
Paul, I recognize and appreciate that you have much greater experience than I do and normally I'd bow to that but the pictures Paul S. posted shows screw holes in the backs of the head above the existing machine plate which seem to indicate that there were tuners on it that were mounted the other way around at some point. Beside that, my snakehead is the other way around and it hasn't been modified. I don't know how to reconcile what you are saying with that I see.
I'm editing this to say that a quick search on the internet netted me pictures of snakeheads with tuners mounted both ways. I found three on the Elderly site with tuners mounted like mine. All have the (cheap) square steel plate and steel gears.
I understand that Gibson has been known to mix up thing a bit on productions runs. Some of these instruments have no script on the head, some have it at an angle and some have it squared up on the head. I suggest that perhaps Gibson sometime mounted the tuners with the peg up and sometimes down. If that is the case Paul can still switch the heads around which should help his tuning problem and still be original.