You will need to copy the appropriate .shp files from the stock sea folder of each ship and place it in the corresponding folder in TMO. Time consuming and a bit of a PITA. IMHO, not sure why one would want to do this, defeats purpose of TMO as a mod to some degree, but to each their own
As marco pointed out, would go with the upgraded version of TMO so can take advantage of lots of great features, including the interior mod recently released.