link2sd was probably taking ownership of the partition. that's why the permission denials. the rest working properly? did you run a2sd check again? you should still navigate to /system/etc and delete install-recovery.sh to avoid mounting conflicts. the swap partition is not used so that should be 0MB when partitioning. if you haven't installed anything yet, partition in cwm again with 0 swap. you're just wasting space there. then just reboot and see where you're at.