So I thought it would be a good idea to update this thread again in case anyone else comes looking for the same question I had.
So originally I had been following these steps: Clone the VM, Copy the cloned files off to USB using SCP, Take the USB to the recovery site and copy back using SCP, Manually edit the VMDK files so the UUIDs match those in the production site (it gets changes during the clone process). It's a bit long winded as the copy process takes a while and editing the VMDK files is a bit of a pain.
In the end I used Veeam's free VeeamZip tool. The advantages being that:
- I could take a backup of a live VM which seemed faster than copying the files off with SCP
- I didn't have to waste disk space on the production datastores with temporary copies of all the VMs
- VeeamZip compressed the VMs very well (so more on the USB I took to the DR site)
- The disk UUIDs were retained so no hacking about in the files required at the DR site
So.... I'm sure there will be functionality built into later versions of vSphere Replicat but, for the moment, if you need to pre-seed a DR site for use with vSphere Replication, definately have a look at using VeeamZip. It made my life much easier.
P.s. No, I don't work for Veeam... it's just a very useful and free tool 
Dave