Cydia (jailbreak issue)

Hi I was very happily using factory unlocked iPhone 5 jailbroken untill one day a msg on whatsapp sent my phone to crash. It just would not come on and ultimately showed me to connect to itunes to restore. I could not restore as iOS 6 had just been released and therefore 5.1.1 was unavailable. I tried to download it from the other sites and restore but got errors of 3194, 21 & 1600. I used redsn0w jailbreak again and was finally able to get the phone working again only to find that all cydia apps not working and not showing as installed though they are showing on the screen and not working. Some apps showed that mobile substrate was not installed/working. I tried installing it manually and the phone again crashed and refused to boot. I had to use redsn0w again to boot. I am now unable to remove the cydia apps and unable to uninstall any of them. Pls advice as to how I should get cydia working with all my apps and/or remove it completely so that I can do a fresh install again.