got this working, fairly simple after all. Order is important however, set your vCPU speed first then the guarantees otherwise setting the vCPU speed will set your guarantee to 100%
#Set the vCPU Core Speed
$orgVdc.ExtensionData.VCpuInMhz = '2400'
$orgVdc.ExtensionData.UpdateServerData()
#Set Org VDC CPU and Memory guarantees
Get-OrgVdc $orgvDCName | Set-OrgVdc -CpuGuaranteedPercent 5
Get-OrgVdc $orgvDCName | Set-OrgVdc -MemoryGuaranteedPercent 5