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Yes, a misadjusted TPS will cause idle problems.<p>Photos of your manifold would be nice to try to solve your other problems.<p>Why didn't you go with a Millenia manifold? The 2.5 Probe IM has smaller ports than the ZE.

The holes you pluged are probably collant lines. Some probe guys had a problem with that because there is a valve in there that opens up an air passage when the throttle body is cold.