I'm glad you asked about Myha!
So the colored stones: they're hidden in the stasis pod. I don't know exactly where you are near the end, but you should be able to reach this device through a kind of tunnel, after opening the last portal with a password.
When you are in front of the stasis pod, you have to do some pixel hunt to find a hatch on the metallic structure on the left. The cursor will change, it's a small hotspot (probably the most unfair part of the game...)
Inside this hatch you'll find the next puzzle and the colored stones.
If you liked Myha after you finish it, you might be happy to discover "Myha Realtime", a fanmade project in full 3D, created by Denis Martin with the Unreal game engine (Denis is the creator of the RoonSehv series, which I highly recommend to Mystholic people!).
Myha Realtime is a free game he made in 6 days for the BlackCube Jam in last December, so it's not a remake of the original Myha (yet), but it's interesting to discover the Myha island differently I think
It's more a technical demo, but it's cool, just like realMyst!
Anyway you can find 6 short free games in total, all created during the BlackCube Jam here (including Myha Realtime):http://jams.gamejolt.io/blackcube2016/games
I highly recommend playing also: The Ruins of Riddoh, and "3"
I hope to read your opinion about Catyph soon! Let me know what you think. Good luck and have fun!
PS: Thanks a lot to my friend Paupasia who told me about your message here (I would probably have seen it much later without her notification).
Please everyone if you have questions and if I don't reply, get in touch with me directly by email, and I will do my best to help you!