1) Yes they were or they wouldn't have been cleared, your understanding of Temp files is clearly lacking.
2) STAGE 1: Tempclean
Internet Explorer cleanup Runs built-in Windows tool to clean and reset Internet Explorer ( rundll32.exe inetcpl.cpl,ClearMyTracksByProcess 4351 ). Runs on IE 7 and up
TempFileCleanup.bat Script I wrote to clean some areas that other tools seem to miss. Note: it specifically targets, among other things, any .txt or .bat files at the root of C:\
CCLeaner CCLeaner utility by Piriform. Used to clean temp files before running AV scanners
BleachBit BleachBit utility. Used to clean temp files before running AV scanners
Cleanup duplicate downloads Searches for and delete duplicate files found in the Downloads folders of each user profile (ChromeInstaller(1).exe, ChromeInstaller(2)exe, etc). Does not touch any other folders. Uses Sentex's Find Dupe utility
USB Device cleanup Uninstalls unused or not present USB devices from the system (non-existent thumb drives, etc). Uses drivecleanup.exe from Uwe Sieber ( www.uwe-sieber.de )
Clear Windows event logs Backs up Windows event logs to the LOGPATH directory, then clears all log files
Clear Windows Update cache Purges uninstaller files for already-installed Windows Updates. Typically frees up quite a bit of space
3) Sure, about the same time as you pay a sizable sum for the pleasure of using a tool without reading it's instructions.