Why not just restore and re-jailbreak using another (less crippled) tool than blackra1n
I'm pretty sure that the ClearCydiaCache program also requires AFC2 to be enabled. Blackra1n does not enable this by default, you need to have installed AFC2Add from Cydia to get this working.
Your other option is to build a SSH ramdisk and boot that, then create a shell script that runs on first startup, it should run the following commands.
Code:
dpkg --configure -a
apt-get update
apt-get install cydia
apt-get install cydia --fix-missing
apt-get upgrade
reboot
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