Just had a look at CRS config … and it’s lacking a lot vith regards to VLAN setup. Did you ever go through this tutorial? http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1 Read the “router” section, that’s what CRS should become eventually.
The biggest issue: bridge1 CPU-facing port has to be tagged member of all VLANs where switch is supposed to route between.
Same goes for bond1 (I’m guessing thete will be some tagged VLANs passing between CRS and L009).