It's hard to tell from the small images, but it looks to me like the gearbox hole isn't clear. Maybe it has part of the broken shear bolt stuck to the side. I have a couple of suggestions:
1. Does the PTO connector slide on the gearbox shaft? To me, that's the first thing to ensure, or else the holes will never align.
2. Use a nail set or other hardened tool to tap on whatever is occluding the hole, to see if you can break it loose.
3. Use a coarse round file to see if you can file away some or all of whatever is occluding the hole. You need to get that gearbox shaft hole completely cleared.
4. Once the gearbox shaft hole is clear, can you insert the new shear bolt? If not, as someone else suggested, tap a tapered round tool into the hole to slide the PTO connector until the holes align. I've attached a photo of a Stanley tapered punch I've used to align holes, but it's just over 1/2" diameter. Maybe you could insert it, then hammer it sideways to move the PTO connector. Or, use any tapered tool, such as the masonry drill in the photo. Insert the handle into the hold until the tapered end hits, then hammer on the tapered end. Or grind a taper on the end of any piece of steel 3/4" diameter or larger, and hammer that into the holes.
I hope this helps.
--- Mike