The root contents seem to be ok. What is the payload you're injecting, and what are you using to inject it? Or are you using a modchip? Considering you're using a Mac, try to set the archive bit in Hekate (Tools > Arch Bit (bottom right)).
Edit: Re-reading your post, I think I can assume you're using a modchip (red boot.dat is the hint). I don't have a modchip myself, but reading this
page of the guide, in that case, you would just rename your hekate_ctcaer_6.2.1.bin to payload.bin. That should let you boot to hekate. As for the payload to install in the /bootloader/payloads/ folder, I would just put plain old fusee.bin. You can get it from the Atmosphere zip file you downloaded earlier. It's in the Atmosphere folder, and it's called reboot_payload.bin. Copy that file to the /bootloader/payloads/ folder and rename it fusee.bin. Then when you launch Hekate, you can then launch fusee.bin (atmosphere CFW in fact). Don't forget to also install
sys-patch.