The inboard shifter level came loose while riding this weekend. I was able to tighten it to finish the ride but not in the same position. Once at home, I tried to reposition the level in the same position I originally had it but it wouldn't tighten down.

Can the shifter rod be repaired like a cross threaded bolt or does this mean the shifter rod and the shift lever need to be replaced? Or, does the shifter rod just need to be replaced? Is this a common issue?

 

It is a very common problem.
Once it gets loose you are screwed.
The entire primary drive and inner primary need to be removed just to access the lever, it cannot be removed . If you install a new lever on the ruined shaft even if it tightens down it will become loose.
Options:
Replace shaft and lever.
Weld existing lever to shaft.
Better Lever. http://betterlever.com/how_to.php

Previous owner of my current bike neglected to check this lever and it was slightly loos when I got it. I cleaned, replaced bolt, locktighted and tightened it down, 10k later it was loose, I went with the better lever route because there was no reason to open the primary and I am lazy. The better lever is a quality item and fixed the issue.

 

Ouch! That betterlever is pricey, but I guess if you really don't want to pull the primary its a good alternative.

 

I am not sure what labor would be to perform the job but I bet it is a good bit. I do not have the specialty tools to do the job at this time so the betterlever was my best choice. At least I will never again have to think about it becoming loose again.
One of the hazards of a used bike I suppose.