I've never heard of a 4.6 shooting plugs. Now 5.4's on the other hand...
And yes there is still a 2 valve 4.6. It is now the base engine in the F-150. It is also the only engine used in the panthers (crown vic, grand marquis).
Having owned a few, I really like the 4.6 in crown vics. It's the perfect engine for that car. However, like the 302 before it, they don't really belong in a truck.
As for the base F-150 engines, replacing the 300 with the 4.2 is the single absolute most stupid thing Ford ever did. I can understand needing a modern engine for emissions reasons, but the replacement should be at half as good as the engine it is replacing. My parents have 99 with the 4.2. I do all the maintenance on it. What a worthless POS engine. Not only is everything on it a poor design, but it's painfully slow throughout the RPM range, can't pull a trailer worth a crap, and on top of that can't manage to get more than 16 mpg in a 2wd 5-spd truck.
As for the 5.4 vs. 351, I think it's a fair replacement. It's got all the torque in the same RPM range plus more HP to boot. They do spit plugs, but I've still seen plenty with over 200000 miles on them running fine.