I recently read that starting in late 2003 that a new 5.4 engine was developed with three values per cylinder,
and was introduced in the F Series Pick-ups in 2004:

I want to know how to be exact that I know I have a new three value cylinder engine. Will the VIN # tell me?
From reading about them it appears that the letter L in the 2004 model should be the new engine, but have found
2002 & 2003 with that VIN letter.

Can anyone help me, I'm confused.

If you own a 5.4 3v, the engine takes a square air filter that unclips with two tabs in the front and will most likely say 5.4 3V Across the top on the induction system. If it is only a 2V engine it will take a round air filter that is mounted closer to the left hand fender of the engine compartment.