The EGR and smog system are seperate. If the smog pump is deleted you will get those codes and it shouldn't cause any problem. The egr does not connect to the exhaust. Exhaust gases are moved through the intake and the EGR valve controls there release. So there shouldn't be anything connected to the EGr valve itself. Your idle problems are being caused by something else...vacuum leak, TPS, IAC, MAF, timing. These are just the first places to look.