I believe the MD50 is a pretty stout transmission for anything a Ranger can do. I have towed my race car all over the country with one at a towed weight of around 4,000 lbs and another 800 lbs on the bed. The main weak point in the MD50 is 5th rear. I understand it is not very well lubricated and towing in 5th is hard on it. That is the only problem I have had with that transmission with over 300K miles on it.
As to the brakes, my 2002 has the smaller rotors and I am pretty sure the 2003 model year had larger rotors. I considered going to the larger brakes, but too much was involved. I went to higher performance pads and shoes to improve stopping power. I now run Akebono ceramic pads and the original Raybestos Super Stop shoes that I installed 250K miles ago. The factory brakes were scary even without towing. With the upgraded pad and shoes along with electric trailer brakes, I normally tow around 72 mph and do not feel the need for better brakes.
I have helper air bags to keep the rear from dropping. It very much stabilizes the tow. Not as well as a weight distribution hitch but still very good.
I had 4.10 gears when I was running 31" tires and went to 4.56 gears with 33" tires. The 4.0 SOHC engine has good torque and does not need to run at high rpm to have good power. I just ease out from a stop without revving the engine. I do slip the clutch a little from a stop but not for very long. I have never burned out a clutch. Starting on an incline is more of an issue when towing. If it is too steep, I will drop it into low range until I get to a more manageable incline.
Finding a new MD50 is not going to happen. Even finding a good, remanufactured one is hard to do. If you can find someone that knows what they are doing with these transmissions, a rebuild is good way to go. Most of the parts are now aftermarket and not as good as OEM.