Have an old Win2003 server with 1 SCSI hard drive partitioned as follows:

D: boot (includes D:\ntldr, boot.ini, etc.)
C: system (includes C:\WINDOWS)

Want to move the whole system to new hardware with bigger drives and different controllers. Specifically, C: to a 300GB SAS drive, and D: to a 2TB SATA drive.

Tried:

VMWare Converter -> VMWare Server -> Diskpart
Result: Diskpart refuses to resize system or boot disks

VMWare Converter -> VMWare Server -> GParted
Result: Will not boot (see http://serverfault.com/questions/219868/resize-ntfs-system-partitions-with-gparted )

Attach original VMWare disk to a duplicate VMWare install -> Diskpart
Result: Will not boot (goes to Directory Services Restore mode)

Backup Exec System Recovery Server Edition 2010 with Restore Anywhere
(tried restoring both to VMWare and to the bare system, without VMWare)
Result: Windows Boot error: Could not read from the selected boot disk. Check boot path.

Supposedly this is a boot.ini problem, so I try bootcfg /rebuild from the recovery console. Says it can't find windows partition so it can't rebuild.

Thought about Ghost but it's completely different hardware/controllers that we're restoring to, so I doubt it would boot.

Reinstalling Windows from scratch is not an option due to critical custom software heavily embedded on the original machine.

Has anyone been in a similar situation (with unusual boot/system partitions) before and figured out how to resize onto different disks?