Vi är vakna nu = we are awake now
Vi vaknar nu = now we are waking up
The first one explains the state we are in now using an adjective (vakna/awake). Vakna could be replaced with any adjective, like "trötta" (tired) or "glada" (happy).
In the second one we are in the process of waking up using a verb (vaknar). It's something we are doing, an activity. You could also replace that verb with any other verb like "sover" (sleeping) or "springer" (running).
In Swedish you might want to add "just nu" or "håller på att" to emphasise that you are doing something in this very moment. Your last examples would look like this:
Jag håller på att ställa en fråga = I am asking a question
Jag ställer en fråga just nu = I am asking a question right now
Other examples with verbs (anything that ends with -er):
It is snowing = det snöar
The aeroplane is flying = flygplanet flyger
My legs are hurting = mina ben värker
We are singing = vi sjunger
I hope I answered your question!