2004 6-speed- I'm not able to pull a code (or that's what auto zone tells me) since the check engine light doesn't stay on..... it isn't on until I stomp it and get to high rpm. Cant I still pull a banked code from it?

I'm sure its some misfire but not sure why. I've just got this thing running after a clogged cat made the previous think engine was blown. I replaced all coils, plugs, and wires, seafoamed it and still no fix.