I would have recessed the nutserts into the skid and removed the 1/8" shims. Except that I had already replaced the six center skid frame bolts with counter sunk flat heads. Doing both won't work because the new bolts would have bottomed out against the nutserts before clamping the skid plate to the frame. The answer there is to eliminate the nutserts and through bolt the frame with sleeves.
If I were to choose one or the other, I would pick the counter sunk bolts long before recessing the nutserts. The greater value being the smooth surface to ride across.
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Is there any advantage to not just opening the hole for the body mount in the C brackets? Cut up a little so the body mount still slips through. Couldn’t you just bolt everything back together like it was before you raised the body mounts?