I have little experience with SPi, but it looks to me like the throttle is being measured as more open at warm idle than it should.
be.
Perhaps this is correct as I do not have an SPi to check. As you indicated, the lost motion adjustment and the stepper may need attention.
Swapping the lambda sesnor is always a pain even on the MPi where you can almost get to it. It would be worth getting it swapped.