Hi - Have the exact same problem.
In fact, there are two electrically controlled/connected vacum valves on the front of this engine. Denso branded part. The one on the RHS goes to the EGR, the one on the LHS feeds a vacum-operated valve which connects to what appears to be an idle/air control on the air inlet manifold.
A problem with the left valve will cause the engine to run roughly.
You can stop the problem (as I discovered), by just disconnecting the electrical lead. It has a captive connector so it will require insertion of a flat screwdriver at a single point.
In the longer term, I would recommend replacement of this vacum valve. My local Toyota dealer quoted me over £330 for a replacement valve part so I looked online. Ebay. On my 2005 model, the correct valve part number is 25819-33010 / 139700 - 0790
However, I saw a very similar part - see part number below - which appears to work OK, and only cost £35 inc postage.
JOb Done - Engine now runs sweet and smooth.
Cloversmate
25819-33030 139700-0970
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