Wow, not sure what's going on with your eggs, but so great there are some signs of life in them again! :)
And YAY for your hubby getting you a real incubator! Sounds like you put in a great effort to build one yourself, but those tend to be alot harder to maintain proper temperature and humidity in. And not sure if your eggs are getting enough oxygen in there? Seems like they are covered by alot of layers from your explanation? They do need proper air flow to develop properly as well.
Anyway, fingers are all crossed for you that you still get some babies out of those eggs! ^-^
Oh, and I agree with always making sure you gather all the eggs you want to incubate first, and then putting them all in the incubator at the same time. You don't want all different hatch dates again like you have now. That makes lock-down and hand-raising them all alot harder if they hatch on different days and are different ages. Older ones will pick on younger ones and all that.