link2sd was probably taking ownership of the partition. that's why the permission denials.i lost the link2d with the wipe and didnt reload it ...so its gone
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.
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