Cool Jeep setup! You're making the right move swapping to a Taco though!
I have an F150 and the best thing I have added is a RimRock toolbox,
Custom Fabricated Truck Equipment | Rimrock Manufacturing. This allows me to access all my tools even when the bed is loaded. They are superior to the Decked boxes in my opinion because they can hold so much more weight on top of them. For the F150 short bed and the Tacoma I think these style boxes are the way to go because a normal style toolbox takes up so much of your already small bed. If you're interested let me know, I liked them so much that I became a dealer.
I have a cap on my truck. I would say that is essential for the type of rig you are describing so that you can lock it up and walk away and not be too worried about your gear. I got really tired of having to keep an eye on my truck everywhere I went. As
@greeniguana mentioned, definitely get one with the sides that open. My bed is steel with bedliner on it, so it is not good on my knees. I keep a small dollar store knee pad in the back to make kneeling back there much more comfortable (yes I am getting old).
I carry tanks up against the cab either upright or on their side. If they are all 7 inch tanks I will use a tank rack or two strapped down to the toolbox. If I am bringing some 8 inch tanks then I lay them all on their side and strap them to the top of the toolbox. I think 14 is the most I have ever had stacked in there. Wagon, gear boxes, and ice chest go behind the tanks.
Something I have been working on but don't have complete yet, is a wash down setup. I have a square, 9 gallon tank that fits nicely by the tailgate. I am hooking it to a small 12v pump and a garden hose to have a fresh water wash down station.
One other thing you might consider is airbags for the rear of the tacoma. If you are talking about loading it down for a class or a weekend of tech diving you might have it squatted pretty good. I have airbags on my F150 and it definitely makes a positive difference when I get it loaded down.
I'll try to snap a picture of my setup when I get loaded this weekend. It's nothing super customized which I like because I do use my truck for work also so I can't have a dedicated scuba only truck.
Good luck!
