Major Gaming System Upgrades and OS-Impact Advice

Hi Guys and Gals. I've looked around and found a few posts with similar questions but feel like my specific circumstances differ enough to make a new one.

So I am upgrading my gaming machine with new case, PSU, more RAM and a second GPU.
Here is my existing machine parts list (this was my first ever PC build); http://uk.pcpartpicker.com/p/BgT94D

The SSD and the 2TB Seagate drive are for my Windows 10 Pro installation/Storage and the 1TB WD Blue is my Ubuntu Gnome Installation.

And here is what I'm changing/adding;
MoBo change to MSI 990FXA Gaming Edition
Additional GTX 760 Twin Frozr in SLI
Corsair RM1000 PSU (I plan on watercooling in the future)
Corsair Obsidian 750D Case
Addition 16GB (2x8GB) Corsair Vengeance PRO DDR3 (1866)

I'm also looking at upgrading the CPU in the near future to an AMD 9590 Black Edition.

Okay now allow me to arrive at my conundrum .. the windows 10 installation. If I change out that Mobo, I imagine my windows drive will throw an absolute wobbler. This OS was purchased as Win8.1 Pro originally and therefore the key I have is for 8.1pro.
(the Ubuntu gnome drive can be ignored at this point because I can simply re-install that once all the other stuff is done)

What I am asking is what my plan should be here?

What should I expect to be presented with when changing that Mobo out, connecting everything back together in the new case and powering it on?

Is there anything I need to do to prep?

Is there an order in which I should do these things?

Is it worth waiting until I can afford the new CPU and doing it all at once, or is it actually better to change these core components one by one when it comes to Microsoft?

If you've managed to read this far without shooting yourself in the head, thank you and I'd appreciate your thoughts :)

The CPU upgrade is not worth the money. While waiting for Zen, you could overclock your existing one.
And I would not go dual card but one more powerful one.

Sorry I should have mentioned this in the original post; I've already bought all the hardware except the new CPU.

You shouldn't need to worry about Windows or Ubuntu, both shoudl be fine with you swapping hardware. What may happen - depending on your Windows licence, is that you might have to reactivate Windows. This is easy enough to do over the phone or via the mobile app they send you a link for. This usually happens when you swap either the mobo, processor or both - so you might have to do it twice if you upgrade in two steps.

Okay cool! Thanks :)