The Honda website has a model library which covers all model specs and options from 98-present. Here is the link.

Honda Model Library

To answer your question, every EX model has a sunroof. It is not an option, in order to get a sunroof you need to buy an EX. Leather is available as an option in EX models only. Having a 5 speed and leather are not mutually exclusive. It is possible to have the 5 speed w/ leather. And it will be one sweet combination! Good luck finding one.