I would cautious about placing a single chick with ducklings. Ducklings grow much faster than chicks, splash water, and trample whatever is in the way.
It is not unusual for one hen to be the "target" of the roosters. Sometimes it comes from the hens behavior such as not accepting initial advances or self isolation making them like a stranger to the flock. Other times it can be hormonal vibes that the hen gives off.
I would suggest making...
I don't have a lot of experience with this situation, but I believe a yolk sack would be more yellow. If it was a yolk sack it would continue to be absorbed. Hopefully someone more familiar with this will chime in soon.
Since your hen mostly laid through molt, it might be her system is due for a break. Hopefully the soft shells don't cause any serious problems and hopefully her system will take a break and reset soon.
Since comb color is influenced by hormones any type of illness could be causing the pale comb. I agree the black specks are likely from other birds pecking him.
Most likely it has more to do with egg quality of individual hens than the incubation, but there are a few connections possible. First where were the eggs in the Incubator? We're the ones from the same hen together. If this is the case there is a chance there was a more suitable temperature...
I have not needed to do this, but ducklings frequently need more niacin which is a B vitamin. (There are many). For ducklings a liquid B complex that is normally used as a cattle injection is given orally. I am not familiar with what type of B is needed here, but I wonder if the complex would...
How is he doing today? Was he with other drakes in the pen? If so injury vs eating something bad is likely.
Unfortunately I don't know anything for if he got into something bad other than fluids and removing him from doing it again.
Maybe someone who does will chime in.
Was this morning the first you noticed any off? With the sudden onset I'm wondering if he could have gotten into something poisonous. Is anyone else in the flock acting strangely?