I sold the M5 Dixie cutter until about 18 years ago, and I didn't remember that it required a pin through the tractor shaft.
Does your tractor pto shaft have a groove around the circumference? Go to Woodsequipment.com and look up manuals for your model. You will see that although the yoke appears to have a hole in the side, it also has a spring loaded push pin that locks into the groove on the pto shaft. So you don't need to drill the pto yoke.
Funny you should mention that. The shaft has obviously been bodged up at some point. It looks like it has a welded-solid small slip clutch at the tractor end. And the yoke on the tractor end only has a single hole in it, i.e., the hole doesn't go through both sides. No push pin, though. Maybe the single hole was for the push pin?
Oh, and I've solved my tech difficulties and can now show you a picture of the slip clutch that was under the shield:

Do you know any way to determine whether the clutch works, short of running the mower into a rock?
P.S. Yes, the shaft with the slip clutch is partially removed from the gearbox shaft. We removed the bolt and we're working on removing the shaft.