Completely stock, without consideration for mods, the better engine is the 4.6(hopefully a 99+). As far as stock engines go, the 4.6 modular is a much more efficient power plant. This engine is way happier at rpms than the 5.0 ever was stock. I agree, when $ is a factor for modding and repairs, the 5.0 is the better value(at least right now). Engine to engine,stock to stock, the 99+ 4.6's are a LOT better engines and a lot happier engines at rpm. I have had a lot of experience with both motors.
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02 S281E Saleen

 

Go with the 5.0 my friend....It's much more reliable 96-98 stang produce a little bit more power..but you can get alot more mods with the 5.0 than the 4.6.

 

wow...not true at all

 

The more you add into a system the more can go wrong, 5.0's are simpler. You also can't look at how many people have problems with a new 4.6 compared to a 5.0 cause chances are the 5.0's got higher miles and is certainly older. If you had a 4.6 and 5.0 with the same miles in the same condition I doubt there would be any real differance in reliability. Also people seem to forget money is always a factor. If you have, say 10,000 to spend on a car you can get a fox in much better condition for that then you could get a new one.