The port in the intake was clogged, if its not allowing the gas back in the o2 wont see the correct change even though it is calling for it resulting in lean condition right?
Nope. The egr reintroduces small amounts of exhaust into the intake stream, it really has none of the same properties of raw fuel. But the O2 sensor reads the air/fuel ratio and signals the ecm to adjust accordingly. So even if the egr was supposed to be adding fuel to the intake but wasn't, the ecm wouldn't lean it out because it was anticipating added fuel from the egr. The O2 sensor would tell it to do otherwise. But it really doesn't matter anyway, because it's spent gasses being recirculated, not fuel.
The ports can be blocked causing a restriction in flow, but still have flow. The same crap that blocks the ports can make the egr stick and not fully close. This is where the driveability issues come from. The egr valve cannot be open during many conditions.
I've probably explained that horribly. But I do know from experience that a completely blocked egr, onop but closed egr, or deleted egr will not cause a drivebility issue. But will occasionally set an "egr, lack of flow" code under certain driving conditions. And deleting a smog pump will create zero issues at all.