If I understood your question correctly, this is actually the expected behavior from converting the disk from P2V, you get the same partitions and data within the partitions inside a VHD/VHDX file. When you attach the newly created VHD/VHDX image file into your computer, the drive letters will be different than what they were originally been using on the original disk.
From your image, assuming that Disk 0 is the base drive you're trying to convert into a virtual disk, do the following:
- On Disk 1, the 39 GB partition, assign a drive letter and confirm that the files and folders are the same on Disk 0, partition C:, if the files are the same, then the conversion completed successfully for this drive.
- On Disk 1, Drive D, if there is no files in there, just delete the partition.
- Create a new VM and attached the newly created disk to it, boot it and you should have a replica of the physical machine as a VM.
I would be more worried about the Windows 2003 compatibility with Hyper-V, you need to install the integration tools: https://technet.microsoft.com/en-us/library/243b5705-96c9-4ec7-9ec5-c68a22b0d42d