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Only if it has a hole in it. Perhaps you've grown a customed to the lack of EGR flow, so now that it works correctly (I hope) it makes noise.
I know you've already replaced the EGR, but did you clean the upper plenum and TB when you did that? Cleaning those components and maybe giving the EGR port a shot of the cleaner might have resolved the EGR issue. How bad off was the EGR... pretty corroded?
I cleaned out the upper intake plenum that the TB and EGR bolt to when I went with a larger TB. It was like night and day in terms of the interior look... now it's a nice metallic color. If you do clean it, use a TB cleaner and not a carb cleaner. The plenum has a teflon coating (yet soot sticks to it ).
you probably had an egr code because of the dpfe sensor(there has been a number of problems with them) the lean codes come from the misfiring cylinders.
Heres and update for you. I think its fixed. Right now the truck runs with no codes and have road tested it once so far. I will keep my fingers crossed.
I did find the vaccum leak too! You won't believe it. Me being stupid. On the left side of the tb there is a vac line that goes into the upper plenum area. This is covered with wire loom. I thought it was just some wires. When I took another look and closer I realized that it was a vac line that had become disconnected. I reconnected it and what do you know, no more air leak.
So far so good. I do appreciate your help, with your answers you guys help me troubleshoot this and think its fixed