Have it tested to give you direction on how to handle it and/or put your mind to rest.

Not all black mold is dangerous(unless there is an allergy situation). Use a mold cleaner(spray areas) and get the roof finished and the windows/doors installed.

It's black and it's probably mold, but it doesn't mean that it's the "toxic" type of black mold. Lot's of molds are black and are not the toxic type. The type people typically are most concerned about is actually a greenish black color.

This is what the CDC has to say about it: https://www.cdc.gov/mold/stachy.htm#Q4

I think you need to clean it, and let it dry out. I don't see the need to pull it all out. In our last house a neighbor had just started building. They were not yet under roof. We had a 1000 year rain (18 or more inches in less than 24 hours). They never had a mold problem. The framing and flooring all dried out.

What does the inspector say?

Here is another link about mold. Luckily I'd read this so when a "mold professional" delivered quotes of 14-27 Thousand $ to demo our basement (without rebuilding a thing) I knew they were full of crap.

Incidentally, when it was demoed by an honest and hardworking contractor, he found NO mold. But that is another story...

Mold info

Also: I found this link here. That Home Site, saving my butt again!

Get a small pump sprayer and Spray with bleach. If it is mold it will change color when it dies. If house is that open it will dry out.

I had mold. Spent a bit of money getting rid of it. When I talked to my dad in Ireland, he chuckled and said "none of died from mold". We live with damp in Ireland, lol.

I would be way more worried about the contractor and his lack of progress on your home than the mold. If he can't get the subs to work on your house that is a red flag in my opinion. We are in a hot construction market and trades may be delayed by several days but they do come and complete the work. We've also had delays due to a rainy spring and summer but the work is progressing with only a 3-4 week delay from early estimates.

I would be more concerned with a contractor using the wrong type of OSB for sub-flooring than mold. Looking at the photos it appears to be swelling and separating already. Should have used something like AdvanTech Flooring, I have saw water stand on it for over a month and not hurt it.

Speaking of mold. I wish I still had the photos.. Bought a 40lb bucket of USG Top Coat sheet rock mud. Used approx 1/3 of it on a job. Two weeks later went to use the same bucket of mud and the entire top of it was cover in a thick layer of Black Mold. Makes me wonder if dry wall mud can form black mold in a sealed container in just two weeks, What are we putting on our walls?

When your house is under roof and dried out, that mold is screwed.

By now, the OP is moved in and living happily ever after.

Burn it with fire.