There aren't any 'stability issues' with a lifted wrangler. Manual or auto, you put the transfer case in neutral and leave it in gear. The input shafts have oilers that keeps the bearings lubed - both drive shafts will turn going down the road.
I had a '03 TJ lifted 6" with 35's and airlockers. Towed just fine but was heavier than sin - it had a lot of armor and guards, bumpers, racks, etc. was about 4200lbs loaded.
There is an advantage to putting locking hubs on the front. The Dana 30 (stock axle) will turn both axles, the R&P, and the driveshaft. It's not a problem, but there is some added drag. Mileage with a jeep is not that great, this is one of the reasons. The downside to them is twofold: the hubs are small so they tend to break if you wheel hard, and they are expensive - about a grand for the conversion. And then you have the rear axle doing the same thing, I have even heard of guys putting hubs on the rear too.
BTW, Currie Enterprises has tow-bar connect peices that bolt to the front bumper/frame for about $100. Works better than a baseplate because they don't hang down in front. Custom bumpers can have tabs welded on to connect a towbar as well.
I bought a trailer wiring kit and ran it back along the frame to the taillights and installed an extra set of 1157 bulb sockets. That way you don't have to tap into any of the electrical on the jeep.
I didn't have brakes on mine, but I have a Brakebuddy for my current toad (new style Scion xB) and it's a necessary safety feature. I had one panic stop with the jeep; it did it but it bent the tow bar tabs and I could smell burning rubber from the RV tires.