The 5.0 is a pushrod V8. I don't know if I have to explain what that is, but if I do let me know. The 5.0 will be cheaper and easier to work on. Although the later 5.0's were computerized, the computer did not control everything. Even in the last year of the 5.0 Mustangs (1995) you could still adjust the timing with a timing light. The 5.0 is considered to have more torque in stock form and because of it's age and popularity has a massive aftermarket.
The 4.6 is an over head cam engine. The 4.6L engine uses a more advance computer and a bigger (the 4.6L block is actually bigger than the 302 block) block. Although it has been on the market for 7 years (originally introduced in the mustang in 1996) there seams to be a lag in aftermarket parts availabiliy. Although this is starting to change now. These engines are not as easy to work on and tuning items like changing timing are not possible with out a computer chip or timing adjuster.
That is just a brief look at the 2 engines, I'm sure you'll get a ton of guys who have actually worked on the 4.6L (I'm limited to the 5.0L) to respond.
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