Without even paying any particular attention to it, I stumbled upon the secret Crystal Ship in my first ever playthrough. I heard that getting the ship is somewhat difficult, so here are some guidelines on how to obtain the ship.
First, make sure that your sectors are lining up in a order that at least makes obtaining the ship possible. You will want a chain of green (sector 5) > green (6) > red (7). Why is this? In order to obtain the ship you must travel from an Engi controlled space (green) to a Zoltan controlled space (green) and finally to the Rock Homeworld (red). If you don't have a combination like this, then you may end up obtaining/waking the pod in Sector 7 instead, making the quest impossible.
To make your life easier, get a long-range scanner as soon as possible. I don't think any particular upgrade in subsystems/systems is necessary, but I personally had level 2 sensors and teleporter.
In the Engi controlled space, search for beacons without hostile ships or stores (long-range scanner can tell you that). Eventually you will find a crystal ship, and you will get the option to grab the weapon/ammo or a damaged stasis pod. Choose the latter, you will need a free augmentation slot to take it.
Next in Zoltan controlled space, again search for beacons without hostile ships or stores. You may eventually come across some friendly Zoltans, who will offer you a third option to repair the damaged stasis pod, if you have it. Repair the pod and you will get a new crew, make sure you take him.
Finally in Rock Homeworld, once again search for beacons without hostile ships or stores. If you are lucky, you will find a transmitter reasonably soon, which will add a quest marker onto your star chart. Follow the quest marker and you will get your ship.
Good luck!
PS: I didn't have a rock man with me, but I did have an Engi and a Zoltan.
