Hooray for taking on a job that seems so huge. Babysteps will see it through.
So, to answer out of order:
b) Half the stuff is in scattered in several different places
Get it all in the same place. If you want to start with clear containers first, so much the better, but just move it all together.
c) Every time your toddler goes in there he wants to eat the cat food

Don't worry about it. Cat food won't hurt him

our DD ate the cat food too. We just got upset when she decided to put all the cat food in their water bowl. It becomes inedible quickly.
a) It's craft supplies and you are a home educating ex-teacher
Good luck! I have a hard enough time with my weaving supplies. A wire rack/shelf and see through tubs (WITH LIDS) really helped me. If the lid doesn't fit, get a larger container or an annex container

Sometimes I feel like I need to take my own advice.

Maryann