I'm still working on the bot concepts but feel that it might be easier to actually have a visual of the basic shape that will be transforming. It should then be easier to see where bits will actually transform from and which bits I hadn't thought about could be used.
The best thing would probably be to create a physical version so you can easily move it about.
Anyways here's the start of the junk ship hull. I'm thinking that a lot of the underside curve can be used as armour above the actual main bot shape. Also the bot ending up looking like wood planks should be fun!