I've never really heard of anyone having issues with IAB's sticking (They're the 4 butterfly valves in the intake manifold that open up to allow for dual runners by the way). They're vacuum operated, so would only not function properly if you have a vac leak, or if they were gunked up, but that's unlikely.
Spray carb cleaner all around the intake manfold with the engine running to check for any vac leaks in general.
Otherwise, it could be an O2 sensor defunking. Unlikely to be the EGR, but you may as well clean it if it hasn't been cleaned for a while, and you may as well clean the IACV as well whilst you're at it.
That hole in the downpipe/exhaust could definitely be causing an issue, back pressures and all.
What kind of a flat spot is it? One that throws you forward in the seat slightly, or just no acceleration when you want it?
Congratulations to vtecmec for winning May/June's Lude Of The Month, with his DIY Turbo BB1 build.
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- NafemanNathan
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