I just had my 87' smogged here in southern California. First run through I passed but there was a bend in the flange on my fuel filler spout and the guy failed me on visual inspection. Sucked because i passed the low pressure evap test they run on the vehicles fuel system. I fixed the filler pipe, went back, and I failed on my NOx levels! Had to take it to a garage to have my local mechanic figgure out what the hell was going on with the rediculously complicated vacuum/egr system. Turned out that my fifth gear switch was sticking on my transmission. It bypasses the EGR valve when you're in overdrive, mine was randomly bypassing the EGR when I wasn't in over drive. He bypassed the vacuum switching valve for that and I took it back and passed my smog test... again.
Your EGR sytem could be having an issue with any number of things, from the pre-EGR controller, the over-drive bypass vacuum switch, the Exhaust gas supply, the vacuum to the EGR valve, of course the EGR valve itself...
I have a Thorley header with a 2 inch exhaust and didn't have any issues with the EGR being unable to draw gasses from my exhaust system. The EGR should Draw exhaust with the engines intake vacuum, not have it pushed into the intake from exhaust backpressure. With those of you who have had success changing out your header or reducing the exhaust diameter, the only thing I can think of is that, If the line from the exhaust is coaked up with carbon then the added backpressure from the stock exhaust may have assisted the EGR in getting the circulation it needed.