I think your fundamental problem is you're using an allowable strain/life curve but trying to analyze with stress/life analysis.
I think you need to be consistent ...
either get strain output from your FEM (directly or indirectly from stress/E) or
convert your strain /life curve to stress/life (by strain*E).
Now the problem would be if you have plastic strains, but then your life will be very short (< 1000 cycles ?), then I'd go with the strain approach.
Why do you say "the software doesn't allow strain-life fatigue curve" ? Do you mean your in-house fatigue analysis is stress based. ok, write a new analysis procedure that is strain based, because strain is the correct data for your specific job. If mgmt question this, ask them what to do. Reckon they'll say "convert strain data to stress".
"Hoffen wir mal, dass alles gut geht !"
General Paulus, Nov 1942, outside Stalingrad after the launch of Operation Uranus.