Sirefef.AC in \WINDOWS\system32\logmein.dll and Cleaman.G in:
\Documents and Settings\NetworkService\Application Data\Sun\Java\Deployment\cache\6.0\54\5249dcf6-5cfa10c5
\Documents and Settings\NetworkService\Application Data\Sun\Java\Deployment\cache\6.0\54\5249dcf6-6267edb0
Combofix was finally able to delete the locked $NTUninstallXXXX$ directory after the MSSec scan but TDSS picked up 4 infected files on one of the recent scans. I have subsequently upgraded JAVA to the latest release as a remediation attempt.
I have attached all relevant logs including that last TDSS log that detected something (no detections now) and the various CF logs.
I can get into the system now but I do not have any networking and I believe that there might be other parts still lingering.
Thank you in advance for your help.