This is why I'm asking for truespace. Time and time again people keep telling me to get blendwer to export to a .cob and thery link me a million different sites with the same damn thing and full python installs and crap, I try it with six billion variations and it never, ever EVER works.
EVER
Err, it's not that hard.

1) Get Python 2.5 installed:
http://www.python.org/ftp/python/2.5.2/python-2.5.2.msi2) Grab that Full hierarchy export script from Water above, and place the .py file in the
".blender\scripts" folder.
3) Before you export your ship, first apply scale and rotation for all objects by selecting them all and pressing ctrl+A
4) If you haven't already, assemble your hierarchy now, by selecting turrets and subobjects first, and the LOD they're attached to last. Press ctrl+P to make all the selected objects children of the thing you selected last.
5) Finally, select everything (turrets, subobjects etc), again selecting LOD0 last, and export to COB using "File>Export>Truespace Hierarchy -FS2-"
6) Convert with PCS2.
As a final note, the script exports to COB with a 1:1 scale, meaning one blender unit is one TS meter, so it's very easy to get the final scale right.