Okay, i've had a lot of trial and errors with this, This is the best solution we've come up with, i have migrated 5 servers (compeltely remotely) successfully using this method:
Create shadow protect backups of each parition on the physical server (be sure to either stop services or use the recovery ISO Before doing this).
Make these avaliable to the new server.
When creating drives on the esxi server, Make C Drive on the first virtual SATA Port. D Drive on the second, and the tiny 100mb EFI Partition as the third or last drive if you have more than one drive.
Restore each shadow protect image (i used the shadow protect recovery boot disk) - Selecting the MBR Tickbox when restoring for each partition.
You Need to set C Drive as an active partition and run MBR / bootrec fixes. These can be done with any Windows 7 or Server 2008 DIsks.
Boot into the disks, load up command prompt.
Use diskpart to set the C Parition as active (List disk, select disk, list partition, select partition, active)
Remane the old BCD File in C:\boot\bcd
bootrec /fixboot
bootrec /FixMbr
bootrec /scanos - should detect the windows partitions (C And D should have the right letters for this to work)
boorec /rebuildbcd - This will recreate the BCD File we deleted with a fresh copy. Windows should now be bootable (make sure vmware boots to the First Sata parition as default (The C Drive of the server - where windows is).
If windows blue screens on boot - Either use Shadow protect to finalise a HIR Restore or vCentre converter to configure the machine. This should resolve the blue screens.
Remove all of the old drivers from the old computer clean up and fix any remaining issues. Install Vmware Tools etc
I Hope this helps someone else - there's pretty poor documentation all over the internet about this.