Yea, you need to delete that "System Reserved" partition before you can convert the drive to GPT.
Of course, if you delete it then your OS will not boot anymore.
Windows somehow always manages to install its bootloader (NTLDR & 100MB system reserved partition) on the wrong drive, always. It doesn't care what the BIOS boot order, it doesn't care what the SATA numbers are... if there are 2 drives or more it will install it on the wrong drive.
The only way to avoid it is to unplug ALL drives except one when installing windows. then when you are done plug them back in.
What you should do is:
1. Unplug all drives except the 3TB one.
2. run gparted, deleted all partitions, convert to GPT.
3. Unplug 3TB drive, plug in SSD. Only SSD should be connected.
4. Reinstall windows to SSD.
5. Plug all drives back in.
6. Use Disk Management to partition 3TB drive and to change drive letters as desired.