In my mod, I have an item that has a custom model which I have managed to get to render when held and in 3'd person. My issue is that I can't seem to get it to render the model in my inventory or when the item is thrown. I know it can be done as the rocket launcher from ICBM renders in full 3D and so does some items from mine factory reloaded. Does anyone know how to do this/has done this before?

It should be fairly simple if you just use IItemRenderer.  Just make the Item implement IItemRenderer, make a private variable containing the model you wish to use, the override handleRenderType(), shouldUseRenderHelper(), and renderItem.