Check engine light flashing

P0100 is indicating a problem with the mass air flow sensor. This is most likely the result of the intake you put on it. The P0400 is a problem with the exhaust gas recirculation system. The exhaust flow control is not responding. Either you damaged some wiring or the new exhaust is causing the issue.

The only suggestion I have is to reinstall the OEM parts so it will pass. After that, do what you want. However, federal law prohibits the modification of emission components and requires the vehicle to meet state regulations.