I have a 1992 Marlin, with 250 ox 66s. I've had the boat for six years. I love the boat. I wish I had four strokes. The engines suck up fuel like there is no tomorrow. Are you going offshore? Are you staying local? Are you mostly fishing, cruising?
The new hull on the Marlin came out in 1997. I'm not sure of the difference in ride, but you can call a knowledgeable Grady dealer or customer service to get some more insight.
What I like on my boat is the transom livewell. It is huge and for the fishing that I do, works great. I can keep large fish alive in that box. That works for culling fluke, stripers and other species. The newer Marlins don't have that feature.
What I would check on the older boat would be the thru hulls, electronics (which you didn't mention), the stringers, the transom bracket, stress cracks, delamination, the decks for any soft spots, canvas, windows for leaks, fuel tanks. On the interior/cosmetic side I would check the general appearance of the gel coat, fabrics (curtains and cushions), fridge, stove, bathroom fixtures, etc. Everything costs money to upgrade. Make a list of all items and see their condition. Compare.
In other words, if the older boat is in mint condition in all these areas, I would go with the four strokes. The OX 66's are considered bullet proof, but I have spent $$ this season on a stator and a fuel pump. Things do wear out.