Hi,
Yes you can use D6-D8 for the relay outputs.
No you cannot use pins 1, 9, 14, 16 for inputs. They can only be used for outputs
Inputs can be on pins 10,11,12,13,and 15.
If you look at the diagram in the link, it shows how to daisy chain limit switches so you only need to use a single input.
Cheers,
Peter.