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Ok so I have this fixed half way. Normal boot is still broken for me, but this is how to start substrate manually:
If you start up in "no substrate" mode, so by holding down the volume up button while restarting, you can start substrate and thereby all your tweaks, by simply reinstalling "Cydia Substrate" AND "Substrate Safemode" in Cydia (at the same time! by queuing). Cydia will then promt you to respring, and tada, everything is running. This is on iPhone 4, iOS 6.1.3.
Cydia Substrate might be called "Mobile substrate" for you.

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Answer selected by DerLudi
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