It is important to properly uncompress the pwnage tools in order to get the Cydia works after firmware restore.
Either use the update function in pwnage old version to get the new version or download the .tgz file and double click (using system Archive Utility) to uncompress. Don't use command line or third party software to uncompress the file.
Cydia needs +S right to run.
If you have terminal access, this is how to reinstall Cydia (if crashed) in command line after login root
apt-get remove cydia
apt-get update
apt-get install cydia
to cleanup Cydia cache, run these
rm /var/cache/apt/*bin
apt-get clean
apt-get update