Migrating a 2003 R2 Physical Server to Hyper-V 2012 R2 in 2018....
Here's the details on how I was able to migrate a 2003 R2 server from physical to virtual.
I used Disk2VHD to convert the running physical machine to virtual hard drives. Note: Do not have it prep for the old Virtual Server software and do NOT have it convert to VHDX. I used a temporary disk to copy the physical drives to during the conversion process. I then used a standalone Hyper-V server to mount the OS disk it had converted to VHD.
Use this guide to mount the registry of the server you're converting for offline editing: http://smallvoid.com/article/winnt-offline-registry-edit.html
This post has the details on the changes you need to make to the registry (adding the IDE drivers to support Hyper-V): https://community.spiceworks.com/topic/post/6155494
I used the standalone Hyper-V host to run the virtual machine for the first time. Made sure it booted and everything looked good. I then exported the VM and copied it to our System Center Virtual Machine Library.
I then created a VM on the Cluster using the VHDs that were exported. Installed the virtual machine integration tools and started the virtual machine.
(reg keys from linked article pasted below)
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Control\CriticalDeviceDatabase\pci#ven_8086&dev_7111] "ClassGUID"="{4D36E96A-E325-11CE-BFC1-08002BE10318}" "Service"="intelide"
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Control\CriticalDeviceDatabase\pci#ven_8086&dev_7110&cc_0601] "ClassGUID"="{4D36E97D-E325-11CE-BFC1-08002BE10318}" "Service"="isapnp"
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Control\CriticalDeviceDatabase\primary_ide_channel] "Service"="atapi" "ClassGUID"="{4D36E96A-E325-11CE-BFC1-08002BE10318}"
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Control\CriticalDeviceDatabase\secondary_ide_channel] "Service"="atapi" "ClassGUID"="{4D36E96A-E325-11CE-BFC1-08002BE10318}"
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Services\IntelIde] "ErrorControl"=dword:00000001 "Group"="System Bus Extender" "Start"=dword:00000000 "Tag"=dword:00000004 "Type"=dword:00000001
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Services\PCIIde] "ErrorControl"=dword:00000001 "Group"="System Bus Extender" "Start"=dword:00000000 "Tag"=dword:00000003 "Type"=dword:00000001 "ImagePath"=hex(2):73,00,79,00,73,00,74,00,65,00,6d,00,33,00,32,00,5c,00,44,00,\ 52,00,49,00,56,00,45,00,52,00,53,00,5c,00,70,00,63,00,69,00,69,00,64,00,65,\ 00,2e,00,73,00,79,00,73,00,00,00 "DisplayName"="Standard IDE/ESDI Hard Disk Controller"
[HKEY_LOCAL_MACHINE\TEMP\ControlSet001\Services\atapi] "ErrorControl"=dword:00000001 "Group"="SCSI miniport" "Start"=dword:00000000 "Tag"=dword:00000019 "Type"=dword:00000001 "DisplayName"="Standard IDE/ESDI Hard Disk Controller" "ImagePath"=hex(2):73,00,79,00,73,00,74,00,65,00,6d,00,33,00,32,00,5c,00,44,00,\ 52,00,49,00,56,00,45,00,52,00,53,00,5c,00,61,00,74,00,61,00,70,00,69,00,2e,\ 00,73,00,79,00,73,00,00,00