1999 Ford Mustang Code p0401 and running very poor??

That code is for egr flow restricted you could a blocked egr port.

I checked all the lines going, and coming out of the EGR valve and all seem to be clean.

The best way to check the exhaust and the vacuum port is to start it without the egr valve for a few second's the engine should start to race and you should hear the exhaust leaking.If you do then you know both port's are clear.

Sorry, I dont think I completely understand. Take the egr valve off? Or just take the lines off the dpef sensor?

Yes remove the egr valve and start it without the egr valve for a few second's the engine
should start to race and you should hear the exhaust leaking.If you do then you know both port's are clear.

Ok, so I took the egr valve off, the engine seem to run the same with air coming out of the steel tube. When I put the valve back on, I put vaccum presure onto the vaccum inlet, and the engine start to die. This mean the egr valve is good, right? Could maybe the egr solenoid that the vaccum hoses connect to, has gone bad? BTW, thanks for all the help!!

If the engine ran the same with the valve off tells me the intake port is clogged.The steel tube is the exhaust if the intake port wasn't clogged then when you removed the egr valve and started it the engine would race because you would have a big vacuum leak.Since it didn't then the intake port to the egr valve must be plugged.That would make sense since you have a egr flow code.

That does make alot of sence! Is there a good way to clean the intake port out?

A good way to do that would be to get some carbon cleaner put it in the port let it soak.Then get a piece of speedometer cable fray one end and figure out the length of the port make the cable a little longer then that and cut the non frayed end.Put the non frayed end in the drill and use the cable like a hone to clear the port.