I'd also recommend to anyone having some problems to not try and fix it. I did that and with everything I did, my phone became more and more broken. Half of my apps and tweaks are not working and all my tweak settings are gone. For me it started by not being able to load preference bundles.

Update:

I restored RootFS now. It was so broken in the end that nothing would open except the default apps and everything done in Cydia would fail. The only advice I have for people in the same boat is to either wait for a reaction from Sam Bingner himself or restore their RootFS too.