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The 2 valve 4.6 was available until 2010 in the f150. I am not sure when the 3 valve became available I think 09 but I'm sure someone else can clarify. I have never personally seen phaser issues on a 4.6 3 valve. The later 5.4's did not have nearly as many problems with it as the 04 and 05s so by the time they released the 4.6 3 valve in the trucks the engineers had probably already dealt with it. The Mustang guys could probably give you some info on earlier 4.6 3 valves if your interested as they were in them before f150s.
The 3v 4.6L did not become available in the F-150 until 2009 model year. The 2v version was still the "base" V8 then, (2v 4.6, 3v 4.6, and 3v 5.4). The 2010 model year was the last year for the 2v and 3v 4.6L engine and the 5.4 as well.