Windows is saying the file's infected with: Trojan:Win32/Emali.A!cl
this may be a false +ve as this is quite an old trojan and both the F-Secure and Trend standalone scanners don't detect anything...
You can use the Raw tab in TiTSEd to change the number of storage slots in the ship, just be aware that having too many items in one category will cause the game to stop with an 'uncaught range' error when showing it (I think it only currently allows about 40 items)
Eventually she'll rebel and do something naughty - run away with your ship for a bit, mess up storage, change your computer password etc and then you'll be able to punish her