P1401 and P1409 help

[Tko2v]

This code is coming up, I eliminated the egr sensor when I built the motor but when I drive it sometimes it feels like it's backfiring or just breaking up. I have a SCT tuner that told me these codes but what I don't get is sometimes it drives fine and other times it doesn't. I have the ports blocked and capped so I don't know what else it could be.

Mod list:
Hi-Tech stage 2 cams
.30 over
bolt ons
full exhaust

Any help would be appreciated.

[Tko2v]

I do have a few exhaust leaks...I have a feeling that could be it.

[Fastlane]

They are EGR codes. Did you turn off the EGR sensor in the tune when you eliminated it from the engine?

[Tko2v]

No the sct tuner didn't give me the option. I was curious as to why it isn't running right, I originally thought the codes would've had something to do with it but I realized the eliminated egr shouldn't be the problem. Could the exhaust leaks be the problem is my question now.