Let us know what he canner shows.
If any codes post back code no.
If you are still getting flashing or blinking check engine light it has a miss fire.
Good scanner will show missfires and what cylinder and how many missfires.
What brand fuel pump did you install?
The scanner will show readings that pont to low fuel pressure but best to drive it with a fuel pressure gauge on it to check for proper fuel pressure and always recheck fuel filter.
Another good tool is a engine vacumn gauge.
Also when running rough or missing is to check for wich cylinders are missing.
Let us know how it goes.