I didn't put these in the batch file format, but these are a few more textures that needed fixing in the low-res texture set: The oven/kiln doors all around, the fire pillars in Hate, and the torn tapestries in ToFS.
Code:
transpfx.exe gequip.s3d -mp ovendoor.bmp
transpfx.exe hateplane.s3d -mp fppil4.bmp
transpfx.exe hateplane.s3d -mp fpface.bmp
transpfx.exe frozenshadow_obj.s3d -mp tapestrymayons.bmp