I had an issue with a Small Business Server SBS 2003 to SBS 2008 migration where once everything was up and running, I had problems with Outlook 2007 Clients giving certificate errors.  Also, OWA Outlook Web Access would redirect to http://sites/owa.  The problem was the internal and external URL settings on the various transports in Exchange 2007.  This powershell script helped to fix the problem.  Note, some errors occurred for me but I was able to just step through the code and issue the commands to the Exchange Shell manually to get the job finished.  The main problem was the AutoDiscover Internal URI - once that was fixed the rest fell into place.

# Script to allow you to set all virtual directories to a common name like mail.company.com

Start-Transcript

# Variables

[string]$UMExtend = "/UnifiedMessaging/Service.asmx"
[string]$OABExtend = "/OAB"
[string]$SCPExtend = "/Autodiscover/Autodiscover.xml"
[string]$EWSExtend = "/EWS/Exchange.asmx"
[string]$ConfirmPrompt = "Set this Value? (Y/N)"
[string]$NoChangeForeground = "white"
[string]$NoChangeBackground = "red"

Write-host "This will allow you to set the virtual directories associated with Autodiscover provided services to the name you provide."
Write-host ""
[string]$base = Read-host "Base name of virtual directory (e.g. mail.company.com)"
write-host ""
# =======================================================
# Validate if a third party trusted certificate is being used
# because BITS won't use untrusted certificates
[string]$set = Read-host "Is the certificate being used an internally generated certificate? (Y/N)"
Write-host ""

if ($set -eq "Y")    {
    [string]$OABprefix = "http://"
}    else    {
    [string]$OABprefix = "https://"
}

# =======================================================
# Build the Autodiscover URL and set the SCP Value

Write-host "Setting Autodiscover Service Connection Point" -foregroundcolor Yellow
write-host ""

$SCPURL = "https://" + $base + $SCPExtend

[array]$SCPCurrent = Get-ClientAccessServer

Foreach ($value in $SCPCurrent) {
    Write-host "Looking at Server: " $value.name
    Write-host "Current SCP value: " $value.AutoDiscoverServiceInternalUri.absoluteuri
    Write-host "New SCP Value:     " $SCPURL
    [string]$set = Read-host $ConfirmPrompt
    write-host ""
    
    if ($set -eq "Y")    {
         Set-ClientAccessServer -id $value.identity -AutoDiscoverServiceInternalUri $SCPURL
    }    else {
        write-host "Autodiscover Service Connection Point internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# =======================================================
# Build the EWS URL and set the internal Value

Write-host "Setting Exchange Web Services Virtual Directories" -foregroundcolor Yellow
write-host ""

$EWSURL = "https://" + $base + $EWSExtend

[array]$EWSCurrent = Get-WebServicesVirtualDirectory

Foreach ($value in $EWSCurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $EWSUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-WebServicesVirtualDirectory -id $value.identity -InternalURL $EWSURL
     } else {
        write-host "Exchange Web Services Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
     }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $EWSUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-WebServicesVirtualDirectory -id $value.identity -ExternalURL $EWSURL
    } else {
        write-host "Exchange Web Services Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# ======================================================
# Build the OAB URL and set the internal Value

Write-host "Setting OAB Virtual Directories" -foregroundcolor Yellow
write-host ""

$OABURL = $OABprefix + $base + $OABExtend

[array]$OABCurrent = Get-OABVirtualDirectory

Foreach ($value in $OABcurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $OABUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y")    {
        Set-OABVirtualDirectory -id $value.identity -InternalURL $OABURL
    } else {
        write-host "OAB Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $OABUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-OABVirtualDirectory -id $value.identity -ExternalURL $OABURL
    } else {
        write-host "OAB Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}

# =======================================================
# Build the UM URL and set the internal Value

Write-host "Setting UM Virtual Directories" -foregroundcolor Yellow
write-host ""

$UMURL = "https://" + $base + $UMExtend

[array]$UMCurrent = Get-UMVirtualDirectory

foreach ($value in $UMCurrent) {
    Write-host "Looking at Server: " $value.server
    Write-host "Current Internal Value: " $value.internalURL
    Write-host "New Internal Value:     " $UMUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-UMVirtualDirectory -id $value.identity -InternalURL $UMURL
    } else {
        write-host "UM Virtual Directory internal value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }

    Write-host "Looking at Server: " $value.server
    Write-host "Current External Value: " $value.externalURL
    Write-host "New External Value:     " $UMUrl
    [string]$set = Read-host $ConfirmPrompt
    write-host ""

    if ($set -eq "Y") {
        Set-UMVirtualDirectory -id $value.identity -ExternalURL $UMURL
    } else {
        write-host "UM Virtual Directory external value NOT changed" -foregroundcolor $NoChangeForeground -backgroundcolor $NoChangeBackground
    }
}
Stop-Transcript

(http://www.exchangeninjas.com/set-allvdirs)

As you probably knew, or do now since you are searching for this information, Exchange 2007 requires a UCC Multi-Domain SSL Certificate to properly function.  Here are some tips for setting it up.

-Pick your favorite vendor to purchase the UCC SSL from and make the purchase

-Generate the request from the Exchange 2007 Server.  To do this, open the Management Shell and issue the New-ExchangeCertificate command.  A great tool is provided here: https://www.digicert.com/easy-csr/exchange2007.htm.  You can use this tool to generate the request and it will save the information to a file in the path you can specify or leave default

   For Example:  Lets say we have an Exchange 2007 Server whos Internet Address is mail.rockabilly.com and its local domain address is exch07.rockabilly.local.  I would also include remote.rockabilly.com, rockaserver.rockabilly.local, autodiscover.rockabilly.com, autodiscover.rockabilly.local in the list of requested names.  Feeding this into the tool yields the following request:  "New-ExchangeCertificate -GenerateRequest -Path c:\mail_rockabilly_com.csr -KeySize 2048 -SubjectName "c=US, s=Utah, l=YourTown, o=RockABillyDoodles, ou=IT, cn=mail.rockabilly.com" -DomainName remote.rockabilly.com, pcrserver.rockabilly.local, autodiscover.rockabilly.com, autodiscover.rockabilly.local -PrivateKeyExportable $True"  Copy and paste this request into your Exchange Server Management Shell and it will spit out the request to c:\mail_rockabilly_com.csr.  Open this in Notepad and copy and paste the request into the request fields at the site where you purchased the SSL cert. 

-Once the request is received by the registering entity, an email will be generated to approve this request.  The email will go to the contacts on the WHOIS record for the domain.  Ensure you have access to those email accounts so you can approve the request.

-Once the request is approved and you are able to download the certificate, the next step is to install it into the Exchange 2007 server.

Set-ReceiveConnector "Connector Name" -ProtocolLoggingLevel verbose

Set-SendConnector "Send Connector Name" -ProtocolLoggingLevel verbose

Set-TransportServer "TRANSPORT SERVER NAME" -IntraOrgConnectorProtocolLoggingLevel verbose

Set-TransportServer "TRANSPORT SERVER NAME" -ReceiveProtocolLogPath "C:\New SmtpReceive Log File Directory"

Set-TransportServer "TRANSPORT SERVER NAME" -SendProtocolLogPath "C:\New SmtpSend Log File Directory"

Open the Exchange Management Shell:

# To check the Content Filter configuration, type in:

Get-ContentFilterConfig

# To set the Bypassed Senders (example):

Set-ContentFilterConfig -BypassedSenders donotspamme@calazan.com, jdoe@abc.com

# To set the Bypassed Sender Domains (example):

Set-ContentFilterConfig -BypassedSenderDomains calazan.com, *.xyz.com

Important Note: BypassedSenders and BypassedSenderDomains are multivalued properties. When you use the Set-ContentFilterConfig cmdlet, it will overwrite the values of those properties. If you just need to add more senders or domains, please follow the example below.

# To add Bypassed Senders:

$x = Get-ContentFilterConfig

$x.BypassedSenders += “jsmith@google.com”, “bhope@yahoo.com”

# To remove Bypassed Senders (can only be done one at a time):

$x = Get-ContentFilterConfig

$x.BypassedSenders -= “jsmith@google.com”

# To empty the list:

Set-ContentFilterConfig -BypassedSenders $null