Is the 00-06 trunks all the same??

 

yes. The trunk lid changed slightly in 02 I think, but the trunks are identical.

 

only the center brake light changed shapes when the soft-top gained a glass window (due to US regulations specifying the space between the bottom of the window and the light)

I learned this after I bought my Mugen 3-piece wing which only molds to the first of the center light designs.