When you claim the ambassador title from cstore it drops it in the inventory as a completely blank box in the first empty spot. Mouse over it youll see it. Then right click equip it and it will show up in the list.
Who do you talk to to rename your ship? I've looked all over Earth Spacedock, and can't find it. Someone told me it was the NPC who lets you choose what ship you're flying, but I didn't see the option there.