It's an ancient art passed down from KLR rider to KLR rider. I recently came into some money, so I splurged on the $60 locking trunk from Amazon. Thankfully, it still retains the all-plastic soul of the milk crate. However, it is fancy enough that all my friends keep calling me things like, "moneybags," and asking me to buy them gas or lunch...
Although I have the side cases, I don't use them regularly. My (used) bike came with this top case and I really like it. It's fairly inexpensive. Some of the reviews complain about the base breaking. I remounted mine using a cutting board from Walmart as a spacer and haven't had any issues. I think that top case will work with either the gen2 or gen3 - just passing it along in case you end up needing some additional storage.
It's an Emgo trunk. It mounts on a base plate on top of the rack and it's detachable, so it can be carried as a separate case. It can also be locked. I love it and absolutely recommend it.
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_awd_ujf.wbA0NYNTJ
I got it from amazon, it's large enough to hold my backpack with a 15 inch laptop while I ride. Here's a link
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_apa_i_fqqmEbGV7D95S
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
Really like it. Holding up pretty good. Just bolted the Emgo plate directly to the Stock tail plate. https://i.imgur.com/DKAchoo.jpg
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
Really like it. Holding up pretty good. Just bolted the Emgo plate directly to the Stock tail plate. https://i.imgur.com/POvR91E.jpg
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
It’s a pretty good box. I screwed the Emgo base plate to the Stock tail plate. Just drilled straight through it. It’s holding up really well so far.
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
It’s a pretty good box. I screwed the Emgo base plate to the Stock tail plate. Just drilled straight through it. It’s holding up really well so far.
Emgo 72-32440 Travel Trunk https://www.amazon.com/dp/B000GVD0VE/ref=cm_sw_r_cp_api_iVo3zb7WXJTN9
It’s a pretty good box. I screwed the Emgo base plate to the Stock tail plate. Just drilled straight through it. It’s holding up really well so far. https://i.imgur.com/08oXrbg.jpg
I have the hi-viz nelson riggs dry bags that are like 100 bucks on Amazon. They are a bit deformed from mistreating them, but they keep everything dry and stay put pretty well. I also carry everything I need to dismantle my entire bike and spare parts everywhere. I am over-packed 99% of the time. They have held up to falls and everything. The saddle bags are about twice as big as the crash bars they sit on. So the top part is supported but the bottom sags in and deforms the rigid back of the bag. It works fine, it just looks a little sloppy. I also have the this box mounted on this rack that I am very pleased with for the price. The box is cheap, but it is easily removed, locks (even though its just plastic and can be easily broken into probably), and it doesn't allow any water in even in the heaviest of rain. I have put these to the test, and they have held up for 8000 punishing miles so far.
As for the fuel problem, do you have the stock tank? I use MSR fuel containers that are specifically designed to handle pressurized fuels. I took a couple with me on the TAT, but never needed them with a 5.3 gallon tank. I definitely would have needed one with the stock tank though as I did a span of 180ish miles between fuel stops. So they mostly just get used to catch gas when I take the tank off or do carb work. I would say keep them outside of your duffels if you can just for the sake of everything not smelling like gas.
The most important part of the system is how you attach it. You don't want things moving around because it will destroy them. Even sand in your tent fly bouncing around on the back of the bike will ruin it as I learned when suddenly my tent was no longer water tight after 3000 miles on the back of the bike.
Is it this case? I have the same one on my scooter.
http://www.amazon.com/Emgo-72-32440-Travel-Trunk/dp/B000GVD0VE
I put my helmet and gloves in my Emgo trunk and lock it up. If I'm worried about the location, the trunk detaches from the mounting plate and can be carried as a portable case.