Pump clearance is a known issue with aftermarket rods and with original Porsche rods as Mark has indicated. I think this is one of the reasons Carillo, Pauter, R&R reverses the location of their rod bolts? These rods have the bolt threading into the rod cap and therefore they don't have nuts with the bolts.
Here's a tech bulletin from Carillo
Here's a picture of clearancing the big body of a 964 pump, which is approximately the same size as a 930 or GT3 pump in terms of its shape. That's not to say the 964 pump has the same oil delivery rates as a 930 or GT3 pump
http://forums.pelicanparts.com/911-engine-rebuilding-forum/267356-another-3-6-3-8-rebuild-thread-2.html#post2929771
You can see in the above link that the pump is already clearanced (notice the "dents" where the machining was done) when manufactured and it needs to be clearanced even a little bit more for the aftermarket rods.