To change the workboat size go to bts/asset/xml/art/Civ4ArtDefines_unit, search for workboats, there are 2.
1.Art_Define_Unit_Workboat and
2.Art_Define_Unit_Modern_Workboat.
The<fScale> line is the size in the game, so for regular workboat it is 0.19 for modern it is 0.28 those are the ones you need to change.
First always make a copy of the file you are changing, make the changes in the copy and replace the bts with the copy. good luck.