you are supposed to raise it on the last days of the hatch, I do it on day 18. ill just start from the beginning
the day I set them I have my incubator running between 99.5 and 101 degrees. I don't recommend letting one heat above the 101 degree mark. (I even use this on still air). I run my humidity about 40-45% on the first 17 days. if your using a hovabator or little giant, simpily fill half the water troughs and remove one plug. don't pay attention to your hygrometer.
on day 18 I lay them flat, and raise the humidity to 55-60%, with hovabator or little giant fill all water troughs and remove the second plug.
your humidity may have been your problem, but with everything that happened you done your best; and that is commendable. don't give up trying to incubate over this, it happens to the best of us. with these instructions and little giant incubators most people get 80% or more hatch rates from eggs raised by them.