My tools are mostly in a military mechanic tool bag (large) I picked up at a surplus store. I also have a list on my cell phone (app called Cozi) of all the tools in there so I can quickly see if I have a particular tool or add it if I find necessary. So far it has been more than adequate.

 

http://m.galls.com/galls-original-streetpro-gear-bag

I'm using this at the moment for some tools and recovery gear. There are enough pockets, although small, for some organization and the main compartment has a divider that can be removed depending on how you want to do things.

 

I built up a wood shelf that is bolted down using the loops from the factory for supporting the back seat, which I never use...

I posted it over into the build thread section, its still evolving, I posted a bunch of photos.

matthew