RE: EGR system, Code 33
Code 33 is defined as "PCM did not detect EGR opening when commanded". There's a few possibilities besides the valve or PFE.
When the PCM commands EGR, it sends a ground to the EVR (EGR vacuum regulator) mounted on the bracket on the left rocker cover. This opens, allowing regulated manifold vacuum to apply the EGR. If no vacuum makes it there, the valve cannot open. Check the green line back to the EVR. Is it cracked and leaking or crushed and blocked? At the EVR, remove the double vacuum fitting, start the engine and check for full manifold vacuum at the other line. If it's not there, follow that line back to the intake. Leaking or obstructed?
On a few very rare occasions, I've seen 4.6s with the EGR tube or internal EGR passage in the intake plugged with carbon, but that's easy to test. Let the engine settle to base idle and use your vacuum pump to force the EGR valve open. By about 10"hg the engine should get noticeably rough or stall. If it doesn't, exhaust gas can't get from the exhaust manifold to the intake.
It could be wiring, but check these first.