That would be true if you found an ally that had a check 'Craft Diplomacy 5', but in the more common case 'Charisma Diplomacy' she would get a d6.
making sure I am doing this right, kyra is attempting a diplomacy check say to acquire a ally, she has a d6 for charisma, but since she is not trained in diplomacy she only get a d4 right?
That is correct. 99% of the time, allies with a diplomacy check also have a charisma check and you'll just want to try that instead. But if you have a card that adds to your diplomacy check or something and so you want to go that route then yes, you're stuck with a d4 before cards or powers.
That would be true if you found an ally that had a check 'Craft Diplomacy 5', but in the more common case 'Charisma Diplomacy' she would get a d6.
These two cases are letting you choose to make a craft or diplomacy check, and a charisma or diplomacy check, respectively; in neither case does Kyra get a d6 on her diplomacy check. If it's the charisma/diplomacy check then she can choose to make a charisma check instead of the diplomacy check and get a d6, but she will never get a d6 for the diplomacy check itself.
You can choose from any skill listed, and you treat multiple skills listed above a single number as separate options.
To give an example, if Kyra was trying to acquire Jakardros Sovark she has 4 options:
Dexterity 8 or Ranged 8 or Charisma 6 or Diplomacy 6.
Given her skills, she would roll:
Dexterity 8 (d4)
Ranged 8 (d4)
Charisma 6 (d6)
Diplomacy 6 (d4)
The Dexterity is a listed d4, Ranged and Diplomacy are unlisted so they are d4 as well. Charisma seems like the best option.
But, if there was a card that required her to make a Diplomacy check because Charisma wasn't an option, she'd have to no choice but to use her d4 Diplomacy.