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If it's misfiring AND running lean I'd suggest checking for a vacuum leak. Check the gasket between the manifold and the head, then check the EGR valve and make sure all of the vacuum lines are in good condition. Also verify that the power brake vacuum assist is in good condition and not leaking. A damaged power brake diaphragm can cause the engine to run quite lean.

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Q: What causes a 2000 Lincoln ls to run lean in both ports and still miss fire on cylinder 6 after complete tune up?
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