There was a major redesign in 2004. I had been looking for a few years so this happened right as I was buying. Here is what I can recall off the top of my head.
o teak and holly cabin sole
o transom redesign with fishbox and folddown bench
o livewell moved behind port chair
o flushmount lower box option
o diesel genset option (2003, now only genset available)
o engine moved from 26 to 32 inch centers
o pulpit changed for delta style drop thru windless anchors (free fall)
o new cabin liner and fabrics
o 3 holders on hardtop legs (2003 IIRC)
o new steering wheel (much heavier, ribbed)
o helm layout changes (switches, angled surfaces, etc)
o new cabin door (slides forward rather then folding style)
o top mounted rigger option (2005 or 6 IIRC)
o higher windshield (2005-2006)
o ivory canvas option (2006-2007)
There may be some oithers but these are the major changes. Great boat. All the Marlins are good but every time GW redesigns a model they typically get even better. Witness the 330 changes for 2008.