1998 Saturn SC2 is throwing P0401 code.

Are sure the egr ports are clear both the ports?Thats a short trouble tree for that code egr not working or clogged ports. The best way to see if the ports are clogged is to remove the egr valve start the car up for a few seconds the engine should race and you should hear a loud exhaust leak. Did you do that to make sure the egr ports arent clogged?

I asked if you checked to see if the ports were clear like I check them?Did you check them like that but starting and seeing that the engine raced and you could hear the loud exhaust leak?Jist because you cleaned them doesnt mean that there clear and not clogged or restricted.

Alright on top of the egr valve where the connector goes there should be a part number please post that part number for me.

What is number on the box it came in?The number you gave on the valve doesnt match the number on the autozone website. Also compare the port opens from the egr valve you took the car came with compared to the new valve make sure the opening match in size. Let me know what you find.

The old one that was on the car was it a duralast egr valve also?If not whats that part number?

I remember seeing and hearing about a bulletin that was taking about the wrong year egr valves will bolt up and cause a flow code because the flow rate is different. According to autozones online catalog that is the correct part number atleast on the box itself. It doesnt list the part number you have on the valve itself it only gives the number on the box itself for oart nunbers. So no way of telling if it was missed box all together for that part.I have seen some crazy things in my day. My niece has a 2009 toyota corrolla its the japan built one I got the japan built front brakes to replace them and they didnt fit. Went to the auto parts store and found all the different brand brakes had the japan and american built corolla front brake pads boxed opposite we had to get the american boxed ones those are the ones that fit. Also my friend has a galant 1986 and all the auto parts store have the same listing this tiny little battery that is way too small again wrong listing. Thats why I want you to compare the openings of the valve because anything is possible even with factory parts. So from what I feel is you have the wrong egr valve some how or some how one of the ports are clogged enough to set a flow code. If it was the valve itself or the wiring going to it it shoukd set a different code for that. If you had a tech2 scan tool we could command it open and see if the engine ran real rough at idle and we could check it that way.

You never mentioned the rough idle before?Do you have any idea why it has a rough idle?Vacuum leak possibly?It only runs rough at idle?

Are you sure its running rough and its just not a collasped/torn upper motor mount making it feel like its running rough?The mount over by the valve cover and coolant bottle?

Its really common for those mounts to fail and it will feel like you have a rough idle but its really just a bad mount. Sounds like you should see if that mount is bad.

All you need to do is get a floor jack put a piece of wood between the jack and the oil pan jack up the jack againist the oil pan to hold the weight of the engine then remove the mount.I would get the auto zone mount it comes with studs make sure you replace the studs it comes with.