every time you install/uninstall a tweak, take note in a text file (can be a note in notes, works as well).
or, do that before wiping the phone for a new FW.
when on new FW, refer to the notes and carefully install the tweaks... a few at a time, usually doing reboots on the nastier ones to make sure everything is OK. some will not work, like folder enhancer on 8.3 (yet). when you are satisfied with the setup, restore from backup.
always works for me.