Pulled the carb off and found there are two threaded holes when looking right down the primary bores of the intake. One has a plug in it, the other one doesn't. What are the holes for, and am I right in assuming I should plug the empty one?

 

Actually, those are the EGR gas injector holes, and normally there should be a nozzle screwed into each one of those. Assuming you have an EGR valve blockoff plate installed on the outside of the intake, those ports are already blocked off. A flush allen-head pipe plug would help mitigate the flow disruption, but there is no worry about a leak.

 

I pulled an A4 off of a 307 from an 85 442 and it had this same problem. It also was corroded around the water jackets enough to leak. I started searching for the other EGR tube. Found it wedged in the intake passage. That is when I pulled the intake and installed a cast iron intake from a later 350. I pulled the other tube and plugged both with hex plugs, like Joe said. Later on I ran this intake on a 330, ran like a champ.