I am going through the same calculations for a 23' Steiger Craft. My estimate is that adding approximately 100# at the transom will reduce the freeboard at the cockpit drains by about 1/2 inch. You could check this for your boat by simply adding some weight near the transom equal to the weight difference of the engines.
Yamaha SWS II 250 weighs 534 lbs. Suzuki DF250 weighs in at 580. Difference of 46 pounds. Move your batteries forward and you have offset the difference completely.
The Suzuki is the lightest of the 4S engines, which is why I will likely repower with that engine when (and if!) my SWS dies.