Are you saying that the hole in the clevis pin wouldn't protrude enough above the sheet metal to allow the pins to install?
The sheet metal in that area is roughly .090" thick. I use a .095" washer to QC the depths of the holes that I make for the clevis pins during manufacturing.
If the hole in the clevis pin didn't protrude far enough above the sheet metal, then the most likely possibility that I can think of is that the sheet metal around the hole was slightly concave. This could have been verified using a straight edge. The fix in this case would be to use a small pry bar to massage the sheet metal around the hole to make it flush with the surrounding sheet metal.
I wish that you would have contacted me prior to modifying the clevis pins, I wouldn't want you to have done anything that isn't going to be safe.
Here's an old pic showing the pin and clip installed, back when I was using 7/16" bolts instead of the clevis pins.