How to restore/edit build.prop after rebooting (and phone stuck in reboot loop)?
After a lot of reading and trying various things I've managed to get control over my phone again.

This guide sounds good, but it didn't work for me as I've encountered an error because of my specific device. This might work with others though.

What worked was this guide(which has problems rendering images sometimes).
I've tried first to unlock the bootloader(BLU button in Flashtool) and used the these instructions to obtain the unlock code based on the IMEI. 
After that I've downloaded a stock FTF image (from goo.im), placed in the firmware folder of Flashtool. Then I could flash the FTF to the phone. Also, because I was using Windows 8, had to reboot into trouble shoot more to change an option to allow non signed drivers.

Hope this helps others with similar issues.