In French, to say, “yes, I do,” you’d simply say “oui.” If you want to emphasize that you really do want to go, you could use “bien” as a modifier for intensity (but you’d have to include the original phrase from my understanding):

• Veux-tu aller au magasin ?
• Oui, je veux bien y aller !
• Do you want to go to the store?
• Yes, I DO want to go!

As far as your second example, a neuter pronoun exists:

• N’oubliez pas de sortir les poubelles.
• Je l’ai déjà fait. OR Je les ai déjà sorti.
• Don’t forget to take out the trash.
• I already did (it). OR I already took it out.

The l’ attached to “ai” is the neuter pronoun. Without it, the literal translation is “I already did,” but whom you’re speaking to could very well respond with, “tu as fait quoi ?” meaning, “you did what?” So the neuter pronoun is necessary to avoid any imprecision.

I hope this helps!