Oh okay! Good to hear it was replaced recently.
You can totally remove all that emission stuff that's there, vac lines and all. I did a long while back, even that AFM. I posted pics of that too. Heck, even my cat is gutted.

To disable the fun EGR, simply remove the vac line. I have a kit from BC (member of the board) to eliminate the valve and tube. Looks quite nice.
I'd look at the tubes from the intake manifold to that switch over valve then to the ALDA. Mine were plugged in addition to that valve being bad.
My hands were too large to get the ALDA off with the intake manifold in place and I had to do glowplugs, so it was a no brainer while I was in there. I've had the ALDA on my SD cranked for a year now? No ill effects but more power off a dead stop.