Broke my Windows install after installing Linux

So after Logans switch to Linux, it has inspired me to do the same.
I have used Linux a little before and have to use it now for college.

I downloaded GNOME Ubuntu 14.10 and extracted the ISO on to a 4GB USB, then ran the Wubi installer in Windows 8.1.
After the installation had finished, I rebooted and was promted by the Windows 8 boot manager to select Windows 8.1 or Ubuntu, after selecting Ubuntu it started to boot up then some error occured and I couldn't get in to a terminal or desktop, all I could see was the background and the taskbar. I gave up on that installation and tried to install via the BIOS rather than Windows and installed that on a seperate HDD. When I rebooted I was prompted by GRUB even though my installation for Linux was on a different HDD to my boot drive, but it gave me the option to boot into Windows and I did.
I was sick of Linux at this point and thought I would remove my Linux install by formatiing the HDD that it was installed on.
But it turns out that GRUB hijacked my main boot drive and wont boot into Windows at all, so I've reinstalled Ubuntu on the formated HDD but can't access my Windows 8.1 installation at all. even though the Windows 8.1 drive is selected in the BIOS

Please help.

Edit:
I don't want to format and reinstall Windows, it's still installed with all my stuff, I just want to be able to boot into it.

did u disable fastboot in windows 8.1?

in the future, please refrain from using the Wubi installer to dual boot. It actually installs Ubuntu within the Windows partition. At least it did that last time I used Wubi. It allows you to uninstall Linux from within Windows.

Also, if you have a copy of your Windows install disc, you can boot from the disc into repair mode and use the boot repair option to restore the bootloader.

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I have disabled Windows 8.1 fastboot in my BIOS.
If that is what you mean?

I don't have a disc drive, but I could install Windows on USB drive and fix that.

ur installing linux to a second drive right alongside windows no?

That is correct.

http://itsfoss.com/guide-install-linux-mint-16-dual-boot-windows/ this is the guide i used to install linux alongside windows ita works for every ubuntu distro

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Also if you want to restore the MBR for windows 8.1 follow directions here: https://neosmart.net/wiki/fix-mbr/ it can walk you through the steps

If you have access to Windows 8 installation media like a DVD, you can boot from it and use the repair your computer option to fix the boot loader. It's been a while since I had the same problem, but I believe this is the guide I followed https://neosmart.net/wiki/recovering-windows-bootloader/ .

If you don't have installation media you can make a recovery flash drive. It says how here https://www.raymond.cc/blog/how-to-repair-windows-vista-without-a-vista-dvd-disc/ .

Don't despair. This is definitely a fixable problem.

The above solutions should get your windows install working again.

I have Mint installed on a seperation HDD from my Windows install. Grub will take over at boot, as long as the Linux drive is online. If I unplug it, windows mbr takes over as if the linux install never existed.

This being the case, I will never install linux in a dual boot scenario on the same drive as windows again, it is too much of a pain to revert back. With the low cost of hard drives, I recommend that you install to a seperate drive in the future.

I have installed both Mint and Manjaro this way, both booted in the same way. Cant speak for Ubuntu.

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Basicly if u set ur second hdd as the first hdd in your bios ur system grub will take over and ull have a option to boot to windows. but in the installer if u choose something else u can set up the linux hdd to ur liking and its safer to do so because like Cobra said u could unplug ur linux drive and windows would just boot normal.

follow this site its the best way to install linuxmint and ubuntu. just set up a root partition and a swap and hit install and ur set to go i installed linux over 12 times and havent had a problem

No no no, I have the Windows 8.1 SSD set as No.1 in boot priority, an GRUB still takes control, so I unplugged the Linux HDD and GRUB is still taking control, that's why I said "hijacked" because it shouldn't be doing this

grub gets installed by default to the first drive in the system.

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You has to redo the MBR. Easiest way is to grab a .ISO of windows and boot from that and do a repair

a) At the Install Now screen - Click Repair your computer

b) Click Advanced Options

c) Click Troubleshoot

d) Click Startup repair

e) Follow the on screen instructions