How to obtain Pidgeotite: By completing the quest: King Pidgeot`s Decree. Available after obtaining Zapdos.
How to obtain Ampharosite: By speaking with a guy at rt18, you have to give him an originally Beldum (your Beldum will be taken by the NPC) to protect him from the "men-in-black". After you do he will give you Ampharosite. The guy is hiding among the trees above the center patch of grass. You should be able to spot him easily. If you still can't find him, you should probably trigger the "Men-In-Black" scene by talking to a random guy in the route from wildhaven to strongwater.
How to obtain Tyranitarite: Complete The Lost Treasure of Eons Ago quest. After you've gained access to the Sand Temple, talk to the guy outside to obtain the quest.
Another mega stone you've missed out is Alakazite. However it is not working properly atm.
How to obtain Alakazite: By completing the quest: The Magician's Secret. Available after obtaining Moltres. Talk to the sorcerer in bluegum to get the quest.
Thanks for the hard work!