That all looks normal to me. Stamping wrinkles. Your new floor will have many of the same wrinkles.

You sure you need full floor replacement? From the portions shown in your pics, your floors look pretty darn good...but your pics don't show the usual heavy rust spots.

If you just have a few holes in the foot areas, you may want to seriously consider patch panels instead of full replacement. Butt weld the patches for concourse/invisible repair, or flange edges and lap weld if you're just building a driver. Heckuva lot easier IMO, and less worry about hurting the structure, less need for bracing, etc. A repro floor is never quite as good as the original...