No problem. Since it was your boot drive that failed, you will be replacing it with a new drive unit in the upgraded system. Then you'll be installing Windows on that drive fresh. Here's an important hint for that stage. When you go to install Windows on the new drive, do NOT have any other drive unit installed in your system. Have just that new drive plus any optical drive you might be using installed. This will force the Install Process to place all of the Windows stuff on that one drive, and avoid a possible problem in the future that has caused trouble for some people.
AFTER windows has been installed this way, you can install both your other old HDD units and reboot. Windows will see them, assign them their own letter names, and make them available. IF it happens that you don't like the letters assigned, you can change them in Disk Management.
One other factor you need to know. ALL of the application software will need to be re-Installed under the new Windows on the new C: drive. You see, Installing any software package places information in the Windows Registry files, and the new OS you install will NOT have any of that info from your old system. I realize it is obvious that any software that had been installed on your failed C: drive will need to be Installed again on your new one. But even any software you might have installed before on those other two drives would need to be re-Installed for the Registry entries to be made. This does NOT mean any of your user files - data or configuration stuff, etc. Just actual application software.