There is 1 step missing from the first post, which is, reset the learned value (voltage) for zero opening angle of the EGR valve. In the Subaru workshop manual it calls this the "Compulsory EGR learning" (ie adaption), however it can only be done with a Subaru Select Monitor which is $$. If you are lucky and get a EGR valve that has exactly the same zero voltage, then it wont need to be relearned by the ECU.
Denso (who made the original EGR) details the checks as: When the engine is stopped, the ECU tests then removes voltage from the DC motor inside the EGR and waits for it to settle on the springs. If the sensor voltage once it settles doesn't match the stored value then a counter is incremented. If that counter gets to 2, a P0409 is triggered. the MIL light is lit. If you clear the P0409 with a scantool or FreeSSM, then the counter goes back to zero and you get 2 more engine starts without the P0409.
Replacement EGRs has a HAL3725 chip inside it https://www.micronas.tdk.com/en/system/files/downloads/files/HAL371x_HAL372x_HAL 373x_Programmable_2D_Position_Sensors_with_Arbitrary_Output_Function_1DSH_final.pdf which almost certainly has a different zero possition voltage to the original. The original is fully encased and mechanically different.
I wasn't able to find any scantool, FreeSSM, Romraider or low level SSM1/2/3 method of resetting the memory location storing the learning flags. Disconnecting the power for 30m and doing an idle speed reset that works on petrol cars does not appear to work on my ECU.
In the end I stripped the original ERG down, cleaned it with carb cleaner and discovered that the plastic intermediate gear had old grease and was slightly sticky. (my original code and the reason for replacing the EGR was a P0403 duty cycle code, ie sticking). After cleaning and greasing the valve always returns quickly to the same zero position with no sticking and has been restarted 5 or 6 times with no recurrence of P0409s.
It might still revert to a P0403 or P0409 after a long drive so please, if anyone knows how to trigger a Compulsory EGR learning process without a Select Subaru Monitor, please share. I dont really want to try and persuade a main dealer to reset it for me as I am sure they want to replace the EGR as well and they are 400 GBP new from an official source. (ie not the cheap eBay clones).
I have photos, of the insides of both EGRs, but can't seem to attach.