This topic is quit the controversy. I have a 03 4.0 4x4, and a 06 4.6 4x4. Both geared 355. You will never get the torque out of the 4.0 that you will with the 4.6, and torque is what you need for big tires as well as that low end grunt you will want in the mud or snow. But as blue_goose stated you will run into other drivetrain issues with either engine. Sadly the 3rd gen EX shares the same 5R55 transmission with both the 4.0 and 4.6 engine, and my tranny buddy says the 5R55 is only fit for a mustang. That being said, it's not if the tranny fails it's when the tranny fails you will fork out at the least $1200.00 if you take the tranny out, have your tranny buddy rebuild it, and you put it back in. $2500.00 to $3000.00 if your not so fortunate and have to have a shop do the work. Now all that being said, in 06 the 4.6 got an upgraded tranny. They went with the 6R60, it is a 6 speed with tougher stuff inside, but it's a 4th gen EX, and that's not going to help the 3rd gen guys. If your on a tight budget, and all you can afford is the 4.0 EX with a few inexpensive mods you can make the 4.0 pull almost as good as a stock 4.6. My 4.0 engine has 268,000 miles on it, and I have not had any problem with the engine or the good ol faithful 8.8 rear diff. only the tranny at 182,000 miles. If you look around and use patience you can and will find someone selling a 4.6 for the same price as a 4.0. good luck..
