Correct me if I'm wrong, but from what I understand, you have 3 drives.
Drive 1 is the small SSD;
Drive 2 is the HDD;
Drive 3 is the large SSD;
Your data is on Drive 1, and to transfer it to Drive 3, you move the data to Drive 2, then put Drive 3 in the computer and copy data from Drive 2.
I have two options for how to do this.
1) Get another USB drive (8GB or so), and make a bootable Linux drive. When you boot your computer into Linux, the OS only sees a bunch of files with funny extensions. You can't just copy/paste some files while in Windows because it sees some of the files as important system files that you cannot edit. For help on making a bootable Linux drive, see this website. I have done this exact same method and it works great.
You would then boot your computer into Linux with your drives attached. You can try copying them over by selecting and dragging, but it might not work if your files are user-specific (Desktop, etc). In that case, you could open up Terminal and type "sudo nautilus", which opens another file viewer that you should be able to access your files on.
2) Use a program like Macrium Reflect. For Macrium specifically, it's a really easy process and there is a free 30-day trial.