autopsy Acheron, research capture and containment, do Favor for a Friend and then Catch the Runner.

Ok I'll put that research to the top. I assume Favor for a Friend and Catch the Runner are missions that will pop up

Yes, Favor for a Friend as soon as you research Acheron autopsy.
Catch the Runner as soon as you complete Favor for a Friend

the side effects are temporary ?

The side effects will be removed after a couple of missions (not time). The more missions the higher the chance. Eventually the removal is guaranteed.

Also mech augments reduce delirium cap and wp penalty

It's about difficulty of the missions, if that soldier complets extreme or hard missions and you don't use experimental treatment on him, in a few missions the effect can be removed