The quest is completely possible. Have you tried not using root at all? Just using acid would give you a better chance at killing them before they get to you and using a better level acid would also help perhaps if you arent already.
I'm not sure which flying monsters you are talking about, there are a few but if its javings what I suggested above should work. If you are talking about kipestas you might want to use cold spells.
Afflictions (root and fear) are mostly used for team leveling. They introduce it to you there though so you know what they are and can learn how to use them even if they may not be the best for the mission. It's not necessary to use them.
I'm not sure which flying monsters you are talking about, there are a few but if its javings what I suggested above should work. If you are talking about kipestas you might want to use cold spells.
Afflictions (root and fear) are mostly used for team leveling. They introduce it to you there though so you know what they are and can learn how to use them even if they may not be the best for the mission. It's not necessary to use them.