Software Deployment

I have just deployed Acrobat Reader 9.0.0 upgrade to all of our users. The upgrade consisted of the adobe reader 9 extracted MSI, and a transform file created using the Adobe 9 customisation wizard.
The upgrade is uninstalling adobe reader 8.1.0 (or older) and installing reader 9.0.0 instead.

For users that simply have adobe reader installed onto their machines, the upgrade is going nicely.

However, for users that Adobe Acrobat (creator) installed onto their machines, this has caused the MSI to try and self heal when run from the programs menu.
To explain this further, if the user browsers to a PDF file on their file system, and opens it, it opens with Adobe Acrobat (creator) without issue. Users can also still create PDF files via the office add-ins, or by 'printing' to the Adobe PDF printer.
However, if a user opens Adobe Acrobat via the programs manu, windows installer is triggered and eventually ends in an error looking for a mapped drive where the Adobe Acrobat (creator) was originally installed from.
I have tested with both Adobe Acrobat (creator) 7 and 8 versions and both receive the same error. Upon reviewing the application event log, the following two items are of interest:

Adobe 8:
Event ID 1004
Detection of product '{AC76BA86-1033-F400-BA7E-000000000003}', feature 'ViewerProgramFiles', component '{347553B7-2470-4BDD-A758-09A9BF9B2015}' failed. The resource 'HKEY_CLASSES_ROOT\AcroExch.XDPDoc\CLSID\' does not exist.
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

Event ID 1001
Detection of product '{AC76BA86-1033-F400-BA7E-000000000003}', feature 'ViewerProgramFiles' failed during request for component '{FBF72A88-9ECC-4E27-9EC5-A978DDD03404}'
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

Adobe 7:
Event ID 1001
Detection of product '{AC76BA86-1033-0000-BA7E-100000000002}', feature 'ViewerProgramFiles' failed during request for component '{58B8935E-9E42-42D1-AAE1-9385DBD7E157}'
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

Event ID 1004
Detection of product '{AC76BA86-1033-0000-BA7E-100000000002}', feature 'ViewerProgramFiles', component '{63AE96E3-B075-4F86-AA37-22D21AFAA653}' failed. The resource 'HKEY_CLASSES_ROOT\AcroExch.Sequence\DefaultIcon\' does not exist.
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.

As I do not throughly understand MSI healing, im wondering if someone could help me with what my options are on this one.
I was thinking that perhaps there is a way of 'fooling' the installer, by exporting the registry keys that it is looking for, and importing them into each affected users registry.

I really dont want to have to reinstall Adobe Acrobat on all affected users machines, as these will number in the hundreds.

With Thanks and fingers crossed...

- Scott.