N14 - shudder/flutter

If the filter was clogged the symptoms would get worse as the RPMs increased because of the restriction.

Injector acting up ?

 

Here are some things to check/try than can cause those flutters;
1- make up a test fuel line and go straight from the fuel pump to the tank to eliminate the whole fuel system in case there is air getting sucked in.
2- clean all ECM powers and grounds
3- Load test powers and grounds at ECM connectors.
4- check all injector connectors including rocker box housing pass-throughs
5- Disconnect alternator and road test
6- Try a test engine position sensor
7- take apart and clean the shut down solenoid.
1000-1300 is peak torque, so it will be heavily fuelling. The injector solenoids will demand the most electrical loads at that time and also inject the most fuel. Bad powers and grounds, fuelling or sensors could cause that issue.

 

What Heavyd said,if it's only under load. I would look more toward shut off solenoid and injector trouble.
Disconnect wire from shut off solenoid,turn key on. Touch wire to post on solenoid,you should hear it click,if you hear a thunk a second or two later the plunger is sticking.
Check the fuse to to the right side of the ECM it can cause some funky problems also,if you have a bad ground somewhere else.