I have seen EGR SOV valves not closing completely ..this will effect egr closing.
The test is to put a BB in the vac line between the egr element port and the SOV and run the car for a few days.
No surge = you have narrowed down the cause.

I also do a manual egr test and part of that test is to make sure the egr SNAPS shut.

As the problem came with EGR change, it also possible that you have a simple vac leak anywhere in between the egr and the intake at the engine ..this could be as simple as the mount bolts/gasket at the intake side or a loose fitting of the cross tube from the valve..