Did you also unhook the EGR vacuum line? Have you had your PCM reprogrammed to eliminate EGR?
If the EGR valve is still functioning, its going to let the engine suck in unmetered air, which will cause issues.
Also, when the PCM, if not reprogrammed, commands the EGR on, it also does several things to compensate for the EGR entering the combustion chamber, including a significant amount of spark advance. This needs to be programmed out.
2005 Pontiac GTO