I have read somewhere that the stepped bottom was changed on the 29 fever over the years. Could somebody clue me in on the evolution? I am mainly curious about the single engine boats from the late 90's up.

IIRC, the step size increased considerably in 1998? I have a 1997 single 29' and it has the small step.
Maybe someone else can chime in?

My 2002 29 has a single step as well. I believe the advances in the 2000s were more along the lines of anchor locker, swim ladder and wrap around windshield. However, I'm no hull expert.

No expert here, but owning my 01' for 6 years now and always reading information on this site, the larger step was introduced in 98' like mentioned already, and I believe somewhere around 2000 they started raising x dimensions. My 01' has a listed X on my Reggie report of 19.5 inches with an XR drive. Somewhere around 05-06 they lowered it to 19 inches. I don't believe they made too many changes to the actual hull bottom between 2000 to the end of production.