I have invested heavily in the skills to craft and upgrade, but I cant find any rules on length of time taken or difficulty etc
Where can I find these things?

I think Inquisitor's Handbook from Dark Heresy may have had a section on crafting, but I'm not completely sure, and don't have a copy at hand to check. However ... from what I remember, it wasn't as heavily fleshed out a section as it could have been.

Yes, when dealing with small items you can use those DH rules, and when dealing with ship components (and assuming appropriately-sized workcrews, workspace, and heavy equipment) use component installation times (at least as a baseline). This is not a topic the books covered in detail, which is weird since the books give at least two of the careers the ability to modify starships.

I did put together a house ruled system for crafting a while ago. It seems to work for my group, although it doesn't get a ton of use since there isn't much down-time in the mad dash the campaign has been thus far.

http://community.fantasyflightgames.com/index.php?/topic/88749-item-crafting-rules-peach/