I wanted to add my recent p0400 code reading. About a month ago I did a complete Biodiesel Submerge with my entire intake. Upon reassembly and start up, a new check engine code P0400 appeared. I took the intake apart 4 times since trying to get this thing to clear. Cleaned all the parts associated with the EGR system. I noticed that on the cross over tube that the mechanism that controls the flapper had a sudden pause in movement. This was caused by the biodiesel somewhat drying out the plastic and not letting it move smoothly, or even buildup. Check both flappers on the cross over tube and underside of the intake body that they move smoothly. If they don't, in my case it'll pop the code. I also cleaned out all the electronic connections with cleaner. All codes are now gone.

There's some simple tests that can determine basic EGR functioning. I found that collapsing the EGR would cause the engine to slow in speed, signifying proper functioning. There's a number of things that can cause this. Just keep checking and rechecking.

Good Luck to anyone in the future that like me found this thread useful.