If it's the same clunk I'm thinking of, it's your A/C compressor kicking on. Turn the position selector OFF before you start it, the clunk should go away.
As far as the stall, it may be that the fuel pump hasnt primed long enough, and there isnt enough fuel at the engine.
To solve this problem, turn the key to the ON position for a second or two,(you'll hear the fuel pump whine) then turn it forward to the CRANK position.
My 2006 did this since it was new, as does my buddy's 2008, and even my dad's 2006 F150.
2006 FX4 Level 2. Superlifted with custom Fox shocks..Oxford white. Auto.
Note To Self: 4LO DOES NOT MEAN INVINCIBLE!!