Do the EGR operation check as outlines in the FSM to ensure your EGR valve is working vacuum lines are good to go and hooked up correctly. Then clean the EGR ports in the plenumn. Also make sure the EGR pipe is good to go. A leaky pipe has caused me to fail in the past...Also a Seafoam treatment can help get rid of some carbon in the combustion chambers, which could contribute to higher NOX as well. My 2 Cents..

99 Gen 2.5, fixing blown head gasket
89 SWB- 33's, ARB Front locker, SR rear locker/axle, SR F brakes, winch, WST Offroad Armor all Around, 2.85 Aussie T-case Gears (SOLD)
Sold: (2) 95 SR's, 86 SWB, 90LWB, 91 LWB
-Can Change a timing belt in my sleep..