The pin that is missing is probably better described as a slide. You know the yolks you get on a gearbox shaft to sit in a groove and slide the gears on the shafts - it effectively does that- sits in a groove and is switched from one position to the other by a pin inserted into it, which in turn is connected to a lever on the headstock. The slider is what is missing and needs to be replaced. About 20mm long and smaller dimensions square (I have literally no idea yet-as I haven’t been that far into the machine- maybe 7mm?) it’s the slide that needs to be drilled once made.The back gear pin on my first Raglan was missing. A suitable sized bolt was being used in its place. Slipping in a suitable-sized drill bit should provide a fairly accurate diameter/dimension? Simpler (and cleaner) than messing around with filler. The Raglan, IIRC, was a steel pin with a spring-loaded ball bearing as a detent. I think the pin had a drilling for a key to keep it aligned.
Unless there is damage, I would not be drilling anything away, unnecessarily.