Hello, dear. For the most part, you're doing wonderfully. Some parts don't make a whole lot of sense, but it's getting along quite well.
I would recommend this revision, though:
Hello, everybody!
It's good that you're all on time!
I'm sending this out to tell you that Mr. Atkins called and said that he won't be here today. He has a fever and headaches, and is staying home, since he probably has the flu, but apologizes sincerely for his absence.
It's alright, though, because Mr. Burden will replace him, and we'll all go to the airport to welcome our French students.
He may be late, because he has to get our train tickets and official documents. I hope we won't miss the train.
So, we'll wait here quietly and patiently for him.
I'm not quite sure why you have something about missing the train in there, if it's just for conversation, or what, but that could possibly be left out, if you wish. Otherwise, you didn't spell anything wrong, it's all just grammar and word placement things.
I hope this helps!