I've seen some pretty messy repairs when it comes to shifters. Some are down right dangerous. I will show you the best way to repair a shifter, period. All parts are from my spare Ducati parts and are readily available at ACE Hardware or other hardware stores.
I don't think a lot of explanation is necessary, so I'll let the photos do most of the talking...
...this shifter is in use by wannaducbad (ask him how it's working out after a bit...
This is what I had to work with...
Spare shifter rod, rubber shift boot-thingy plus an allen set screw and a bolt I didn't use...
Cut shift rod and allen bolt from ECU...you can see, here, how I filed the shifter and drilled it for the set screw...
Cut shift rod, allen bolt from ECU, rubber shift boot-thingy, allen set screw from battery tray and...shifter after it was filed and drilled...
be sure to cut the shift rod on the side that has standard threads
I did have to tap the threads all the way through for the allen set screw to bolt in from the other side, but you could just drill through the side without threads until you hit the threads. I would use a drill stop or a bunch of tape and measure it twice before it's too late. That's about them most technical part of this process...