If your intake was clogging , you would slowly lose performance as your airflow through the chamber is reduced. Most likely it would be hard to notice as it's gradual. If you have your intake off, certainly look inside and see if it's gunked up, and clean it.

Here's a pic of a TDI intake after 40K with the stock EGR settings...

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2004 Ram 2500 Cummins HO
2000 Jetta TDI
1999 E300 (sold)