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Swapped my intake manifold on my '98 Civic last weekend and now it runs worse than before

I thought I was being smart upgrading to a Skunk2 Pro Series manifold at my buddy's garage in Fresno. Spent 8 hours getting the old one off, installed the new one, and now it's choking at every stoplight with a CEL code thrown. Anyone else deal with tuning headaches after swapping intakes?
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lisa_brown
Heard this exact same story from my buddy Marco up in Modesto. He threw on a Skunk2 manifold on his '00 hatch and spent two weeks chasing vacuum leaks, ended up having to retune his whole idle air control just to get it to start. Think he snapped one of the coolant line fittings too (the plastic ones, real brittle on those old Honda heads) and had to patch it with JB Weld at 11pm in a AutoZone parking lot.
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