I assume you know that, as with the driver's side seal, the pax side also goes inside the box and not on the outside between the case and the lever? It goes inside the case between the case and the actuating cam. The drawings in the manual show the seal on the outside, which is not the correct location. I am not sure if the actuating rod can be removed from a fully assembled box to change that seal...but give it a try.
Also, the holes for the locator pins to set the solenoid will get you close, but after 60 years all the boxes are worn and will not likely operate correctly if you just put the pin in, set the solenoid and drive. It normally takes a tweak more open to get the boxes to engage and release positively. I set the solenoid by jacking the car and operating the OD with the wheels off the ground. Tweak the setting until you just get positive engagement, and that will give you a positive release too.
If you are force to drill the pin out, you will need a taper ream to repair the hole when you are done. If you bent the drifts, it likely means you are trying to tap a little off center...at an angle.