okay so i fixed this problem on my phone, same exact problem as you. I luckily had openssh and filza downloaded tho. hopefully you have at least ifile or filza downloaded as you can install debs. and install openssh or mobile terminal. i went on it and literally uninstall every single tweak (including mobile substrate and such) then i went into filza and deleted cydia.app and other cydia files i found. I rebooted and reinstalled yalu beta whatever is the latest via cydia impactor. then i went back into a jailbroken state and went to http://apt.saurik.com/beta/cydia-arm64/ and downloaded the latest cydia deb. and installed that. i resprung and when i launched cydia it said preparing system files and thats all.
mobile terminal commands i used
dpkg --list
dpkg --purge (the id thingy i cant remember name)
and thats basically it that i can remember.