Reinstall a clean copy of Mavericks AND migrate my Apps and Settings?
I advise the following:


Make a backup of the current state of the machine, this time using Time Machine's Exclusions Option to remove the offending files (e.g ~/Library/*/python) from the backup.  
Holding down CommandR at the startup chime, boot into OS X Recovery and erase the startup volume using Disk Utility.
Cleanly reinstall OS X on the empty volume
Once complete, use Setup Assistant (not Migration Assistant!) to restore the Time Machine Backup.


Notes:


You can only restore complete backups -not incremental. The TM backup mentioned in (1) must be a complete backup. 
Be wary of what you exclude and only exclude what is necessary. For example, excluding the /System folder will prevent you from performing a full restore via Setup Assistant. 
Why not Migration Assistant? It's prone to cause problems when doing a clean restore.
The Pondini links provided are for Mountain Lion. All the instructions work exactly the same in Mavericks and are completely applicable.