Are you doing EOC by turning the key off or did you install a kill switch? I make a chip that tricks the ECM (when you press a button) into putting the car into Auto-Stop for EOC.
I know you don't have a good IMA battery, but there's a workaround that will allow you to use Auto-Stop (regularly, or with my extra switch) and will also give you Lean Burn.
What you do is you install a clutch switch that tells the car the clutch is engaged to prevent IMA assist. By doing this you can keep the car from trying to use the IMA battery, and therefore the car never learns the IMA is dead, so you don't get a CEL and the IMA light stays off. This unlocks lean burn and Auto-Stop. I can explain this in greater detail if you're interested.
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