Please help - how to upgrade MOBO without issues?

[42trays]

I am upgrading my build from an H97 board to a Z87. I'm keeping everything else the same, including the CPU.

What I could really use is a good step-by-step on what exactly I should be backing up and doing before I start the whole rebuilding process. I have Windows 8.1 installed on an SSD, but there are other program files and stuff on that drive as well. There aren't system files on the two other HDDs I have so I imagine I can just leave them disconnected when I go to reinstall Windows, right?

I still have my Windows key handy.

 

[42trays]

You save any file you want to keep, and you install the ssd hardrive to your new motherboard and start from scratch.
Its boring,its long winded,but with an ssd updates only take a couple of hrs if you limit it to 50 at a time (2 hrs including windows install, probably)and the machine will be reliable.
All that cloning guff is asking for trouble in comparison.
Save any files on the ssd to the other two drives. install windows with only the ssd installed.Connect the storage drives afterwards.

If I copy everything from the SSD, Windows files included, to the other hard drives, and then connect them after the Windows install is done on the SSD, will I run into issues? Or will Windows automatically get rid of previous Windows files? There isn't too much extra on the SSD except for a few documents and program files that I can identify. Should I try to move only the folders/files I want to save, or move it all?