Bootcamp vs rEFIt & rEFInd, mbr, gpt

I've been trying to install Windows 8.1 on Yosemite via Boot Camp Assistant, but got an error:

Windows cannot be installed to this disk. The selected disk has a mbr partition table, On EFI system window can only be installed to GPT disks.

After fighting with rEFIt and rEFInd to overcome the issue (which I then deleted by deleting its folders and its StartupItems file), I came across the instructions how to change the partition tables to GTP via gdisk. So I did that and voila - Windows let me to choose that partition for the installation. My joy lasted as long as the last step of Win setup process when I received an error saying the windows can't modify the boot information. It's now throwing me below error:

Recovery

Your PC needs to be repaired.

The Boot Configuration Data file is missing some required information:

File: \BCD

Error code: 0xc0000034

I've tried few command prompt solutions suggested by Microsoft, which didn't work, like

BCDboot x:\windows /s c: /l en-us

Bootrec /fixmbr

Bootrec /fixboot

Bootrec /scanos

Bootrec /rebuildbcd

The last two commands gave an error "Windows installations found: 0".

I'm lost at that point. There is cleary an issue with remainings of rEFIt / rEFInd, as my computer doesn't boot correctly - it throws an error "No bootable devices found". However, if I press an option key during chime it allows me to pick my OS X SSD, which is now called EFI Boot instead of it's name (EVO SSD).

How can I bring the boot back to normal? Could that be an issue when trying to install Windows?