I got an example drawing that needed to be purged and cleaned using SmartPurger. The problem was that it took forever. Increasing the timeout did not help.
Here was my tip.
I suggest you select only the Purge Regapps using ASDKCleanRegAppARX and set the script timeout to something high like 1000 seconds.
After that you can purge using other options.
Using this tip it still took a few minutes to remove all the Regapps but it helped and it worked even with AutoCAD 2009 as I was using it to confirm this.
This functionality was added with the 2.6 release of SmartPurger as previously described.