Hi all! I'm sorry for the wait back from this post. Unfortunately Cheep passed away on Saturday morning before she could get to the vet. I've decided to get an autopsy so we can guarantee that this is definitely what we are dealing with. I'm still waiting for results - I'll update you when I get them back. I'm heartbroken

All my other budgies seem fine - they are all time so I've been handling them daily and no sign of illness. Maybe Cheep never fully recovered? I know small animals hide illness really well.
I just read back through my post, and I think because I was so frantic and stressed about my babies, I made a few too many errors. I'll go back through each of your questions (and fix up my errors!).
Firstly yes, it is an avian vet!

I am aware the risks of the illness, and have taken heaps of precautions myself (and my family had as well!).
Secondly, yes! All individual breeding cages! I probably should've mentioned that. I read all the risks associated with colony breeding.. and definitely will never support it. Sorry for any misconceptions! I researched for over 12 months before breeding them... I wanted to make sure I was prepared for all situations! Also, I should've mentioned as well that i know three clutches in one year is FAR too many. That was the one thing I wasn't educated about. I believed a friend who has done it for years.. and unfortunately that led to this. I will never breed that many again (I probably won't be breeding budgies again for a long time either - it's more of a hobby and animal loving thing for me!).
I'm unsure of the exact measurements of the avaries. I'll see if I can find them online or I'll measure them tomorrow - i don't like turning on the lights in the room they are in once they are covered for the night. Currently I have 6 in one and 7 in the other. There is heaps of room though!!
Thanks all for your help! And again, I'm sorry for my horrible post before this - I'll definitely make things more clear next time!