What you have looks like it will work from the info you gave about the system. So if there is not any surprises.

On existing machines (systems) that I am going to automate, I get the best human operator I can find to run the machine, then record everything. See what the operator does if a problem comes up and work that into the algorithm.
ON ERROR 1 GOTO FIX 1
IF FIX 1 fails THEN ALARM

You may have the situation where one problem needs fixed with and in dealing with it causes another, so min and max values for the error fixing part.

I do not know about avicultures, but say the gas levels go up and fresh air is needed, and some how because of the weather this drives up the humidity. Can the humidity be higher than the set point for how ever long it takes to bring the gas levels back into range?

Just thoughts...