I also use Macrium all the time and have restored successfully.
Hwever, this from a Macrium forum:
Macrium Reflect has never supported Windows editions previous to Windows XP
I suspect, though, that a Macrium restore CD made on an XP PC might work to boot the Windows 2000 PC to the restore CD boot environment.
Even if you use Macrium to get an image into the guest environment, you will still run into the hard drive controller glitch that MergeIDE fixes. Here's a suggestion about how to run MergeIDE on the original PC without changing the original OS:
Get another hard drive that the original PC can use. Use Macrium booted from a restore CD to clone the original hard drive to the new hard drive. Disconnect the original drive and boot the new hard drive. Run MergeIDE on the OS on the new hard drive. I would also uninstall any custom drivers for hardware, such as special network cards, video cards or mice, and unnecessary software the W2000 has on it now. Shut down and remove the new hard drive. Replace the original hard drive. Now the old W2000 PC is back to the way it was with no changes, and the new drive has a cloned copy of the OS with the MergeIDE edits.
Here's a way to get the W2000 physical drive contents into a virtual drive that Virtualbox can use:
Attach the new hard drive to your Windows 10(? 7 or later will work) PC via USB. Install Macrium on your PC. In Disk Management on your PC, Action menu, click 'Create VHD'. Make a VHD, not a VHDX. I would use fixed-size, since dynamic VHD's have a design flaw that can make the VHD fail with complete data loss if there's a disk error at the right time. Make the VHD the size of the USB-attached disk, plus a few GB. Once the VHD is mounted and you have a new drive letter for it, use Macrium to clone the USB-attached drive to the VHD.
Now unmount the VHD from your PC. Make a Windows 2000 guest in Virtualbox. Here you have a choice. You can use the VHD as the main guest disk, or you can use CloneVDI to make a dynamic VDI copy of the VHD and use the VDI as the guest disk. Virtualbox is compatible with VHDs, but is completely at home with VDIs. I would clone to a VDI, and keep the VHD as a backup.
Boot the W2000 guest, recognize new hardware, and go from there.