Few suggestions for the P0089 and P0090:
1) Check your FPRV with the bottle test
2) Check for bent/damaged fuel lines
3) Verify you have prime at the fuel filter head (open bleed screw and check for bubbles)
4) Check demand vs actual fuel rail pressure
Most common fixes for this seem to be change the fuel filter first (which you did) and otherwise replace the FPRV and fuel pressure sensor.
The P0404 may be a clogged EGR system, but I would just solve that one with an EGR blocker plate and a "fingerstick".
1) Check your FPRV with the bottle test
2) Check for bent/damaged fuel lines
3) Verify you have prime at the fuel filter head (open bleed screw and check for bubbles)
4) Check demand vs actual fuel rail pressure
Most common fixes for this seem to be change the fuel filter first (which you did) and otherwise replace the FPRV and fuel pressure sensor.
The P0404 may be a clogged EGR system, but I would just solve that one with an EGR blocker plate and a "fingerstick".