Consider pulling the drives, so that you can have an AV dedicated computer perform multiple scan's on all of the drives based on schedules.
Please note though that scanning with multiple tools at once can at times cause problems, so your experiences may vary when doing so.
Also consider developing a d7 PE Environment that you can pop cd's into your systems and perform your removal tasks there.
As far as automating it so that you can keep the systems running while you're out of the office, I totally feel your pain there.
What has helped me the most thus far is to automate all of my pre-removal procedures so that if I'm running a Quick Removal, everything up to the actual tool like Malwarebytes, SAS, etc. run's auto no input required. This excludes d7s MalwareScan. Once the Mbam scan kick's off I know that I'll have an 1-2hrs waiting on it to finish. SAS can be about the same, although I feel like it finishes faster than Malwarebytes (I don't have a way to automate it for you, sorry).
I would suggest that you start your primary scan with an AV tool that you know will take the bulk time up front..like Emsisoft a2cmd, Avast aswMBR, or ClamAV...Some Command Line Scanners are listed below...
Avira Command Line Scanner http://www.avira.com/en/download/product/avira-command-line-scanner-scancl
- Usage of Command Line options is covered here: http://www.f-prot.com/support/windows/fpwin_faq/445.html
AVG (may not work with AVG 2013 Command Line Scanner in Safe-mode) read more here: http://www.avg.com/ww-en/faq.pnuid-1285111443
AVG scan can be also started from the commandline (both in Windows and DOS environment) without user interface. This can be used to call and execute the scan from other applications (e.g. Windows Scheduler, Winrar, ...).
AVG scan executable file is located in the installation folder under name avgscana.exe or avgscanx.exe (Default installation folder is C:\Program Files\AVG\AVG10). The avgscan?.exe needs to be started with parameters to specify setting for the scan. You can get list of all parameters by starting it with the /Help parameter or see the following list:
/SCAN - starts scan. You need to specify path to be scanned. e.g. /SCAN=path;path/
/COMP - starts scan of the whole computer
/HEUR - toggles use of heuristic analysis
/EXCLUDE - will exclude path or files from scan e.g. /EXLUDE=path;path/
/@ - specifies path to text file that contains parameters for scan
/EXT - specifies extensions to be scanned e.g /EXT=EXE,DLL/
/NOEXT - exludes extensions from scan e.g. /NOEXT=JPG/
/ARC - toggles archives scanning
/CLEAN - toggles automatic healing
/TRASH - move infected files to the Virus Vault
/QT - starts only Quick test
/LOG - generates a scan result file
/MACROW - toggles macros reportiong
/PWDW - toggles password-protected files reporting
/ARCBOMBSW - toggles archive bombs (repeatedly compressed archives) reporting
/IGNLOCKED - Ignores locked files
/REPORT - saves report to a file specified file
/REPAPPEND - append to the report file
/REPOK - report uninfected files as OK
/NOBREAK - do not allow CTRL-BREAK to abort
/BOOT - enables MBR/BOOT check
/PROC - toggles active processes scanning
/PUP - toggles "Potentially unwanted programs" reporting
/REG - toggles registry scan
/COO - toggles Tracking Cookies scan
/? - displays help on this topic
/HELP - displays help on this topic
/PRIORITY - sets scan priority - Low, Auto or High
/SHUTDOWN - shutdowns computer upon scan completion
/FORCESHUTDOWN - forces computer shutdown upon scan completion
/ADS - toggles scan of Alternate Data Streams (NTFS only)
/HIDDEN - reports files with hidden extension
/INFECTABLEONLY - scans files with infectable extensions only
/THOROUGHSCAN - enables thorough scanning
/CLOUDCHECK - checks for false positives