no, the coolant passages are not different. The reason for the different number is likely the valve cover gasket. The heads, as far as the gaskets are concerned, are essentially identical.
The MLS gaskets have never been specified for our engines. you have to go to a Ford F150 4.0 spec or late model mustang 3.8 to get the part number for the MLS gasket.
See this thread if you want to look at MLS gasket options.
I went with the Felpro Permatorque MLS gasket for the 98 Mustang 3.8. Part Numbers: PN 9262PT and 9263PT