According to the instruction booklet I have, Step 9 is fitting the first of the LE sheeting.
The LE sheeting is attached to the spars and the spars are at the max thickness point of the wing.
Therefore, I would be placing the shims under the LE sheeting at the spars and that should take care of the shim thickness.
I might add that the deep spar material provided in my die cut kit — yes, it's old — was wide enough so I had both pieces laser-cut so that for all but the last couple of bays on the inboard side where the lead-out overlaps, my wing will be a full D-tube. I suggested that to John B as a running change several years ago, but I don't know whether he took it up.