@PyroGameMaster we have same problem.
Try to re-jailbreak first don't do restore yet it will erase everything.
After you re-jailbreak try to open cydia and add some source. If your cydia still working and package content is there then no need to worry you can still install those missing cydia tweaks you want. I know you already know what I mean. I just share my experience.
This is what I have experience on ip5s when some tweaks broke my jb:
First I did re-jailbreak using Pangu app the result is my cydia package content went missing (cydia app is there still working but no package content you can add some source but still no content)
Second I lost my patience so I decided to restore factory settings, the result is cydia app and some app was still there cannot be erase like iCleaner, iFile etc..
Third I did try to restore 10x times the result still the same cydia and other apps still there.
So I notice that when you installed Pangu app and re jailbreak the rest of cydia app is working.
So I just leave it as semi tethered half with Pangu. Cydia is working but no content no tweaks installed.
You can install apps and other appcake apps but no tweaks anymore. I just install some apps with tweaks like facebok++ through cydia impactor.
(sorry for my english )