@patrikshah
I will let @pk comment on the ITIN and dependent aspects. As far as preparing the return, I'm going to recommend you see a tax professional.
It's still not completely clear, but I think you filed a joint return listing your spouse and children, and the IRS adjusted it after you filed. So now you need to essentially file the same joint return, but as an amended return, so the IRS reconsiders your spouse and dependent info.
To do this in turbotax, you have to pay to prepare an original return. That can cost roughly $100-$300, including a state return, and depending if you use the DIY software, Live Assistance (DIY software plus video chat with an expert if you need help) or Full Service (expert does your whole return for you.) Once you have the original return, you can then prepare an amended return.
Any tax pro is going to charge you for an original return first, because they need to input your data and understand your original situation, before they can understand what needs to be amended.
But you have a second problem. Your amended return must use as its base, not the original return you prepared, but the return that is on file with the IRS after adjustments. You didn't download the right transcript for that, although it should be in the system somewhere, and if you want to do it yourself, you need to be able to create an "original" return using Turbotax that matches the adjusted return in the IRS database. Then you can use that as the base for an amended return. This may be difficult for a typical consumer, which is why I think you might be better with a tax pro.
Good luck.
