I'm sorry you lost your soul dog. I lost both of my old dogs this summer and it was really rough. My house seems to quiet with only the 2 I have now.
I'm not sophisticated enough and don't want to spend the time to do the type of organizing you are doing. I did reorganize both my sewing and cutting areas after we put down new flooring. About as far as I get with that type of organizing is to put things in translucent plastic boxes with cards labelling what is in them. It seems to work well enough for me use and took very little time to do. I hang all of my yardage in the closet. I tend to be really visual and have to see things to now what I have so that works well for me too