Just to put down my opinion, since I lvled stuff to 50 too...

I plan on leveling each crafting class to 20 then move each at 5 level intervals. Is that wise?
In my opinion, yes. this is the way to go.
If you have crafters on similar level, you can share clothing. (If their level is too far away you need to have multiple clothing sets to keep up). Since you are already filling up on retainers, no need to make your Armory Chest filled also.

Is it best to pre gather or see what I need for DoH then go out and find the stuff?
I would say no to pre-gather... because some mats will most likely go to waste

Any tips on keeping mats sorted in bags / retainers to make crafting easier?
My bags are pretty messed too, so I can only say about retainer...
Try to categorize your retainer pages in a manner you can remember. (such as "page1: meat/fish, page2: Metal/Jewel" etc)