Yep, I saw step 20 say to use the new nuts, but at step 31 I was thinking 'what smaller nut?' until I realized I was the one I removed in 20. It's no big deal and super obvious once you realize what needs to be done, but I thought I was missing parts for a few seconds.
I did not use a ton of padding on the door sill, just a few MF towels. I'd recommend all future installers to use more