Thank you so much for trying it out, I love to hear that! I'm working on a revision that should clarify some rules and I'll make sure these questions are covered there too.
1. The complication affects the spell you had just cast.
So let's say Spell #2 and #3 are exhausted and my spell dice are on 1 and 6. When I cast spell #1, I would first exhaust spell #1. Then I roll that die. If the result is a 1, 2, or 3, then the spell #1 I just cast would have a complication. If the result is a 4 or 5, the spell works as intended.
If the result is a 6, the spell works as intended AND you get to unexhaust a spell AND you can set that die to any number that isn't 6 (That's the rules definition of a "boon", but it can also be "things go better than expected" in the story.)
2. Yes, if you roll the same number as the spell you just cast, there is always a complication.
When you cast a spell, you always exhaust before rolling. For your example: whether or not spell #1 has been exhausted before you decide to cast the spell, it will always be exhausted when you roll to check for complications.