Wow! Lovely chicks!!
To clean mine I just use an anti bacterial washing up liquid. I don't totally submerge the yellow base. But do make sure to get into the nooks and crannies. As for the lid just blow all the fluff out with a hair drier and every third hatch remove the guard cover to get right in. I also wipe the bits I can get to with anti bac on cloth, dry everything straight away.
Some different colouring on the eggs is sometimes normal Allthough maybe just because they have been stored. Give them a whirl and see what happens some people do get hatches from older eggs. Good luck