So far with everything I've done the 5.4 is pretty similar between 97-03, somewhere in 04 is when the 3V 5.4 started and you have many more differences. I found some differences here and there, I bought a ported intake manifold for a 2001 5.4 and the EGR is a little differently located on my '03 engine. There are probably more minor differences here and there but with a little mod you can get earlier parts to fit.
I used the larger MAC throttle body made for 97-02 on my engine and everything lined up fine with no issues.
My gibson headers are made specifically for 03-04 2V engines so there could be another difference there.