Hole that where the rust went completely through the fabric.
Nymo beading thread, fireline may also be used, basically any beading thread that is designed to be used with sharp and/or metal beads will work well with rusted fabrics.
Crewel or tapestry needle with large eye.
Pearl Cotton for those areas that your machine needle, and threads, absolutely refuses to play nice with, sometimes you just have to think outside of the box!
I prefer Schmetz needles, I typcially use the largest leather needles I can find for my machine.