So after finding great advice, I tackled the fact that my engine was running rough and the P401 code. I pulled the throttle body off and cleaned the severely clogged ports. Made sure to clean everything as I went. Hoses look good. Put together and ran very rough. Went and changed the EGR. Run at speed pretty good but still a slight hesitation, put at idle very very rough. Question 1 - When I took the EGR off, I noticed that the right side bolt had the hose bolted on. The left side did not have a nut. Looks like just a bolt sticking out. Is that broken off? Question 2 - What is my next step?

 

Next question is do you still have any codes after the work?
The roughness is an issue but codes first before going on.

 

No codes. Cleared them all yesterday after putting in the new EGR. Drove 20- 30 miles today, no CEL light on. I have developed what I read as Hooting. Also some hesitation still exists.

 

To be sure the EGR is not causing the roughness, remove the hose.
This makes sure the EGR is closed unless it leaks.
If you still have roughness with no codes and the idle rpm is close to 750 then
a Scanner is the way to look at live data to detect what is close to being out of limits and may be causing the roughness.
It could be a leaking injector, air leak, fuel pressure to high/low etc but not to the point of setting a code.
Even poor gas quality or water in the gas.
Good luck.