I came across the answer finally, I will provide the answer for anyone else who wants to know how to do this.
Changed my customer validator to:
<asp:CustomValidator ID="CustomValidator9" runat="server" ErrorMessage="Please select you height"
ClientValidationFunction = "ValidateHeight" Display="Dynamic" ValidateEmptyText="true"></asp:CustomValidator>
Then my JQuery became
<script type="text/javascript">
function ValidateHeight(sender, args) {
var drpHeight = $('#<%=drpHeight.ClientID%>').val();
if (drpHeight == "CMs") {
if ($('#<%=txtCm.ClientID%>').val().length > 0) {
args.IsValid = true;
return;
}
else {
args.IsValid = false;
return;
}
}
else if (drpHeight == "Feet") {
var drpFeet = $('#<%=drpFeet.ClientID%>').val();
var drpInches = $('#<%=drpInches.ClientID%>').val();
if (drpFeet == -1 || drpInches == -1) {
args.IsValid = false;
return;
}
else {
args.IsValid = true;
return;
}
}
}
</script>