There is no reason not to use your main in the early survival stages, but unlike your regular damage focused team, you will have to pick up healing for once. If you do things right, your entire team should come out undamaged.
For example,:
Kabuto Fire Main
Kakashi x x
GNW Neji x x
Main should use fire ball chase and low float to knockdown summon (this strings all your chase together)
Yes, neji is in move, 4, no it's not a mistake.
While this is a "general" formation, you should adjust formation before each fight such that kakashi clone gets killed in round 1 (or at least the primary tank)
Here is how it goes:
turn 1: use GNW neji AFTER enemy healer/cleanser have moved, if they have one, on the first ordered offensive mystery ninja they have(so not hinata, if that's what they have in slot 1). This will ensure that it *s around for round 2.
turn 2: fire main 2nd mystery on whoever casts a mystery (if you guessed wrong, feel free to restart, AI does the same thing EVERY time, so next time you will KNOW)
When to use kabuto clones? When your kakashi clone dies of course. If it doesn't die when slotted to soak the most of the damage, enemy isn't dealing enough standard attack damage to matter, your kabuto will heal fine. If it does die, look, 2 more bodies to block standard attack. (again, micro adjustment of position is helpful so that the clone actually tank the attacks)
As far as mystery is concerned, between your neji and your combo-to-neji, they shouldn't get any off. And usually, node 1-9 are fairly weak so after just those two rounds, they are half dead. Turn 3? mop up with kakashi going down on whatever can still cast mystery(unless that is in slot 1), that will also lead to neji chase and stop them.
No, the goal of first NINE (not 6, NINE) node is not "let's use a non-main team and it's fine if they die". The goal of the first NINE node is to beat them all without losing a single character and without any significant (>25%) scratch on ANY of your character. This will allow you, for 11 and 12, should you encounter a really tough team, throw an ENTIRE TEAM at it to just kill ONE character off the enemy, so that your main team can come in and mop up the rest. That is how you pass all survival EVERY time. If you waste a sub team early, then you are completely at the mercy of RNG on 11 and 12, if enemy is strong, you will run out of steam and fail.