When seeding basement landing which reads,
2A: Clue 1, Magical Lock
Which "clue" card do I use? 1A?
For the story choice I made would I seed Clue 2A for the Master Bedroom? It reads:
3A: Magic Phrase, Clue 2, Puzzlebox (?), Locked Door
And clue card in the kitchen would 3A, right?
Yup, that's all right.
Lastly, if I set everything up correctly should the investigators find the clues in numerical order? 1A then 2A the lastly 3A?
They'll find the clues in reverse numerical order. The Keeper Guide has text that you read to the investigators at the beginning that hints at where to find the highest-numbered Clue. Then each Clue they find will give them a hint at where to find the next lower Clue and a key they'll need to get there. For instance, the Magic Phrase they get with Clue 2 will unlock the Magical Lock that guards Clue 1.