Skyline sir, you are a God among men. I cannot thank you enough. I had done all the above apart from the Player####.entity. I was searching for a file like that, which listed all the available research for an empire, I just didn't know where to look.
It was the 'Colonise *PlanetType*' which I was adding, and everything had fit in apart from the research showing up.
One other cool thing, when you create research dependancies, it automatically connects them with the arrows on the tree
Thats also handy to know, I came across some references to arrows when looking for the elusive files, and wondered whether I would have to manually design and put them in. Thanks for the tip Annatar.
Once again, thanks for both of your replies, greatly appreciated. Oh, and one last thing, has a Modding Wiki been set up yet for Sins'? It would help a lot of people, me included. And any tricks, tips, and info we find while modding would have a place to be written down.