Derek, it may not be necessary to break into the gearcase. The shift fork is normally under some tension in neutral and usually it'll go right out of alignment as soon as you pull the pivot pin out. If you undo the shifter cable & wiggle the shift lever around, you may be able to get the hole in the side of the fork in view.
Then, you can use a machinist's scribe, scratch awl, ice pick, heck, even a thin nail will do, to 'catch' the edge of that hole and bring it back into alignment.
While you're rasslin' that shift fork, wiggle the shift lever until you find a position where the fork will stay in one place long enough to get the shift fork pivot pin reinstalled.
If, for example, you find you can't get it aligned with with the motor down, try tilting it up, or vice versa. Sometimes that's enough to make the fork move around a bit, into alignment.
Make sure the O-ring/gasket on the pivot pin is in good shape, in a pinch you can spread a thin coating of Permatex #3 Aviation-Type gasket dressing on the threads & the old seal to minimize the possiblity of leaks.
HTH.......ed