emergency core update disabled site nothings redirecting right
Installation and Configuration
This is WRONG and likely your issue:
ln -s jrCore-release-5.4.0b4 jrcore
you probably have "jrCore" and "jrcore". It is CASE SENSITIVE so delete "jrcore".
Is there a reason you don't use the Marketplace to upgrade? It would save you all this headache and hassle.