1. If you always need to make manual adjustments on top of the calibration, I'd recommend you to automate them, run a script after the calibration that adjusts the localPosition/Rotation of the IK targets or whatever it was you needed to adjust, like this:
// Run the calibration, then just call this:
ik.solver.leftLeg.target.localRotation = Quaternion.Euler(leftFootTargetLocalRot);
...with leftFootTargetLocalRot being the Rotation value of the left foot target Transform after you had manually rotated it to your liking.
About the stepping up onto a block, if that glitch happens, does it help if you move the root of the avatar up to the block level? Sorry, haven't seen this issue before, would it be possible for you to record a video of that glitch please?