Which 4.6L should I buy??

If you could car less about which look you want and your goal is to make power, then the '99-'01 Cobra would be your best bet. You heard wrong about the 4V's. Their every bit as easy to mod, but the benefits of the 4V's bigger and better breathing capabilities make them more rewarding. The '99-up Cobra's are better still because they carry an updated higher flowing head and intake than their predecessors.

You’ll get about 35hp out of a PI cam and intake swap alone on a ’96-’98 2V, but you’ll get about 50-55hp out of a full PI cam, head and intake swap.