I have an 04 and it grinds/clunks into 2nd gear. Its definitely worse when it's cold. Went to ford and they supossidly rebuilt it. Same problem remains. Also when in neutral with my foot off the clutch it sounds like there is marbles in the transmission. Ford likes to call this noise gear rollover. Sounds like a POS. Anybody else have gear rollover?
My '04 3650 did the same thing. It is now broken though.