Hey, thanks for posting you guys, I'm glad to see you are enjoying the alpha of the game!
As far as i remember, it's somewere in the tower. I used a Chandelure so i needed that stone :D
You can find a dusk and dawn stone in the clocktower chamber, which is the area accessible past the mysterious door. Unfortunately, you need the Old Key to access this area, which is only obtainable at the end of the current alpha release. However, there also is a small chance that if you talk to your following Pok?mon it will be holding a dusk stone. I believe there is a 5% chance that the item your Pokemon picks up will be a dusk stone.
Also, the availability of fossil Pok?mon and primal reversions was mentioned:
Currently, the player can only obtain the dome and helix fossil at the excavation site. In the upcoming beta release, this will probably be changed along with several other things to make more fossils available. Also, there are no primal reversions for fossil pokemon currently implemented in the game. The only implemented and obtainable primal reversions from the alpha release are listed below (spoiler warning).
Some of you mentioned issues with your following Pok?mon. If you ever encounter this problem, just open the options menu and toggle "disable following Pok?mon" on and off while in the game. This should reset them.
Finally, I would also like to extend a thanks to everyone who has been keeping up with the game. I am currently working very hard to get the Beta 1.0 release out as soon as possible, and many of the glitchy features in the alpha release will be fixed. To help spread the hype for the new release, here's a quick snapshot of a re-sprite that I did. It's gonna be in the upcoming beta!
(**Spoiler warning for those who have not played through the alpha ;)**)
-PokeVec40