1. Create VHD from Hyper-V manager or Disk Management in Server Manager
2. Attach the VHD, initialize with MBR, create volume (format with NTFS and mount to X:\), set active
3. Launch EasyBCD, in "Bootloader Setup" tab, choose correct Partition, and install BCD (a.k.a. PBR, Partition Boot Record)
4. At this stage the newly installed BCD is still empty. Now click "Add New Entry" in EasyBCD with default settings to add a default entry
5. Deploy a OS into the VHD: imagex /apply <path to install.wim> <index of image> X:\
6. Detach the VHD

Now the VHD is a sysprep'ed, bootable, and absolutely clean VHD.