Hey, thanks for playing and commenting!
For your questions, you are correct: you only build one upgrade per front, the prep moves don't add any more upgrades/structures.
And for the prep rolls being really bad, yeah that can happen if you are unlucky with your Bane dice rolls; just make sure you are only adding 1 Bane die to all rolls in Front 2, and 2 Bane dice to all rolls in front 3. The probabilities definitely get tougher in Front 2 and 3, but they aren't impossible.
I try to switch my mindset a bit when I roll poorly, and focus on the tragic story that's unfolding. Will your Pilot sacrifice themselves if things are obviously so dire? How does your home and connection react to the terrifying destruction of the Kaiju? What does it mean to persevere against such terrible odds? What will be left after Front 3?
Hope that helps!