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I installed the DISA and headers. Got similar codes to yours. The first problem found was the O2 sensors were swapped (my fault). We also did the valve cover gasket, but did not replace the Valvetronic motor gasket. A smoke test revealed it was leaking by the gasket...the Valvetronic motor was ok. If your gasket is good, then motor could be bad.
No issues with the intake for me...I changed the gaskets and made sure I connected the cables correctly (triple checked).
The only other suggestion is if you replaced headers, recheck the headers for leaks.
I can't confirm 100%, but my understanding is that the stock program/ecu has the capability to control the 3-stage manifold already...in other words, it should run fine if it is plugged in correctly. If you changed headers, gaskets, ect., then you maybe off chasing engine ghosts now. Personally I gave up after an hour or so of scratching my head and took it to some experts for help. Cost me $200, but they found the issues I had messed up in about 15 minutes.
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