You want to create "offline" an image containing a PE build that can be booted by VirtualBox, right?
Have you ever tried MBRBATCH/MKIMG to create a RAW image?
Try now, use a geometry of 255/63, choose any filesystem you like, if creatng on a NTFS volume use mksparse, if not use fsz.
The image will be bootable (invoking NTLDR) and formatted by the batch, just copy to it any files you need (for tests NTLDR+BOOT.INI will be enough) before closing the Explorer window, VDK will be automatically removed.
Use qemu-img to convert to .vmdk.
Re-mount the converted image with VDK to check.
Try booting it in VMware or Qemu.
Try converting it to .vdi with Vboxmanage or "import" it on Virtualbox, it should work, though there are reports of failure in the conversion.
In case, try again starting from the RAW image and compare the two .vdi's.....
P.S.: the batches already create a .pln file, changing them to create instead a .vmdk descriptor as cdob
suggested is trivial, I also wrote a batch to create a .pln from RAW: http://www.forensicf...m...89&start=30
modifying it should also pose no problem. I am sure you can get the needed parts from my "rude" batches and maybe write a "real" application, if you need help in explaining anything, just let me know.