Sept is a folder from Atmosphere. Not sure what CFW you're running but you'll need that folder from the latest Atmosphere release to run the tool you're attempting to use.
May look at this tonight, I don't think it would be easy. You'd probably have to manually use the --listfiles, --sign, --replacefile options from the original tool.
Depending on what's wrong with it, it may be a simple and cheap fix. For example, if it's the eMMC you can replace the eMMC for about $20 and flash your NAND backup. It should still boot into hekate if it's unpached and will probably tell you.
Thanks for the awesome script, I've made a few changes (both to the script and LibHac) that make it slightly better. It now accepts variable names in the out dir, which are being used to better organize the output for Checkpoint. It saves them in out/{userid}/{titleid}/{saveid} {timestamp}...