If you look up the parts on a Toyota site you will see some of the brackets fit 03-14 and others 03-09. It does look like the running boards themselves are different for 03/04 but I bet they'd still work seeing the brackets are the same, probably just look slightly different.
My limited came with running boards although someone removed them before I got it. I put others I bought on it. Not sure if all models have the holes but you could look. There's 3 brackets per side and each have two bolt holes for bolting onto the angled part of the underside of the floor. Pretty easy to spot.
I believe the side frames for the 03-23 are all similar. The body on top of the frame varies and so something designed for a 5th gen may be a little longer than a 4th gen.
As long as you have all the hardware - any 4th gen parts should go right in. With a little bit of creativity, you should be able to use 5th gen steps, rails too