Backup Exec (V-Ray Edition?) in this scenario

Lets see if I can help answer any of them for you.

Is BE V-R edition the best choice in this scenario?
I think its the best.  You can do IMAGE based backups with file level recover if needed, along with complete recover of the VMDK.

Do we need to licence 2 copies of BE V-R - one for each server?
You need to license based on the sockets in the complete VM environment, so it looks like you have 1 proc in each physical, so yes 2.  See the license guide: http://eval.symantec.com/mktginfo/enterprise/other_resources/backup_exec_licensing_guide_21223660.en-us.pdf

Do we need to licence any additional agents or products?
Don't think so

Would BE V-R be installed onto VM1 or should it be installed on a separate VM (new VM3) or a separate Server entirely (would this affect licensing)
I would recommend installing BE on a separate server with its own disk for backup.

If we later decide to run both servers with either a VM on each or load balanced with the 2 VMs on each in a cluster type scenario does this affect the licensing/set up?
Not with V-Ray license as its per Proc license.

Any other helpful advice
Do some reading on www.backupexec.com and the support site on best practice in backing up VMWare

Is there a pre-sales e-mail (UK/EMEA pref) who can answer this and any other questions if I can't get the answer here.
Not sure about EMEA, but US does.

You can download trialware version of BE and test it for 60days before you purchase it to make sure it does what you want.  Like the other poster, V-Ray Edition is really just BE2012 in a license/price bundle for Virtual Only environemnts.