You need both dowel pins. That top hole looks a bit oblong, like the trans case was moving?
With the transmission apart, you could even check the run out to the trans pump housing in the case and correct it if needed.
For offset dowel pins:
http://www.robbmcperformance.com/products/dowels.html

I would go through the trans and rebuild it. If your mechanically inclined, you could do it for $100-200 depending on the quality of parts used.