Help with scripting

End of the first wave means the script will restart from the beginning I believe. You can change the behaviour of your monster by setting conditions before the "end of first wave" so they will be in the script or after and they could act as counterattacks. You can make conditions such as :

If monster has less than X HP cast spell Y (whatever it is)
or
If variable X is greater/lower than number Y do something else
or
If bit X of variable Y is set/clear then cast a spell or attack or do special attack.
or
If monster is attacked by spell/attack X cast spell Y

Those are only 4 of the many examples. I'm not posting the actual commands because I don't know them by heart and I always forget them lol

For what you want to do you could set "add 1 to variable #2" in your main script and put the condition before "If variable #2 is greater or equal to 1 cast flare". The first turn variable #2 will be at 0 (when the condition is going to be meet) and the second turn it will be at 1 so the second turn and all the subsequent turns your monster will cast flare.

The best way to learn is by checking some script in the games to see what kind of scripts there is and one of the best document about monster script is this one: Final Fantasy VI monster command scripts guide

This document is also handy:FF3 Monster Command Script Tutorial .

Everything is there and with a bit of practice you'll soon be able to do nice scripts. There a people way better than me for monster scripts and I'm not a reference but It's by experimenting with the commands in those documents that I learned.