To make it easier to start the grub screw, simply move the lever it threads into. This will give you a straight shot at the screw hole.
Make sure everything is grease and oil free, and be sure to apply red Loctite to the screw.
Once you get the screw started, release the lever and tighten the screw down by hand with the ball driver. Then take a short Allen socket, with an extension, and torque it to spec while holding the lever so you get a straight shot at the screw. You can now actually use the shift lever to get things lined up. The reason I mention short Allen socket is that you will loose torque if you use a long one due to the bit twisting. Use 3/8 drive tools over 1/4 drive for the same reason.
Don't forget to remove the small freeze plug in the cover so you can poke through that hole to get the detent lever installed when you lower the cover. It's best to replace it and use some Honda or Yamabond to seal it at installation. Just push it in until flush with cover. BTW, if your shift shaft seal is leaking, this is the best time to replace it. A word of caution though, if the grub screw was loose for a while, there will now be a burr around the tapered hole on the shift shaft that the screw fits into. This may make it difficult to remove the shaft.
I once got to do this job twice on the same bike, the second time for free. :mbird
That's when I learned that just screwing it back in and tightening it with a ball driver is not enough.