If you're having issues with the ship.mod file not installing through the patch, you simply need to place the installer and all of it's content into your main game directory and run it from there.
Can't tell you why exactly, but that's what you need to do.
Well.. I found the problem.. and it's really simple!
If you can do a fresh install of this mod and return 'baseitems.2da' to how it was prior to installing this mod (from the backup folder), then read on. If not, and you've installed other mods that change 'baseitems.2da' and it will be too much hassle, then follow the instructions I wrote previously.
What the problem is, is that the patcher tries to install 'bao_armor.uti' twice and gets an error and skips the .uti alteration. What you need to is actually very easy. Assuming this mod is completely removed from your override folder and the 'baseitems.2da' has no reference to the charged armor, then do the following:
1/ Unpack the mod and go into the 'tslpatchdata' folder.
2/ Open 'changes.ini'
3/ Scroll down and find the section '[install_folder0]'.
4/ Find the line 'File3=bao_armor.uti' and delete it completely.
5/ Renumber the next two lines to file 3 and 4 e.g.'File3=231bdur.dlg' and 'File4=equip_bcarmor.ncs'.
6/ That's it, you're done. Save 'changes.ini'.
Install the mod. Now the patcher should install 'bao_armor.uti' and alter it to match the row number in 'baseitems.2da'.
A single line caused so much hassle. Oh well.
Good luck.