So I take it's been factory formatted then? (Please don't follow the guide right now as A9LH is installed to the NAND as it is, you run the risk of doing damage if you do certain things there)
Before you jump doing anything, the system boots normally, just FBI/JKSM are gone? At that point yes, you would need to inject FBI into Health and Safety first, then install it permanently.
Though to do this, you will use Decrypt9 (hold right on d-pad during boot). (assuming you copied the same files back), send me a screenshot of your SD hierarchy)
You'll need to do the following
1. Choose sysNAND options
2. Go down and choose MISCELLANEOUS at the bottom.
3. Choose Health and Safety Dump
4. Name should be HS.APP (press A to continue), you should see a H&S Dump Succeeed. (If you get a H&S Failed De/Encryption Error, let me know)
5. Send me your HS.APP via PM and I'll create an H&S injected app for you.
6. Once you have it, go back into SysNAND options->Misc->H&S inject
7. Press the down arrow to go to FBI_WITH_BANNER.APP (which I'll send to you)
8. Should inject successfully.
9. Reboot the console. It should boot up normally. When you go to the Health and Safety App, it should now be FBI. Run FBI, and then I suggest install the FBI.CIA (you can download from the github or if the CIA folder is still there, you can install from there)
That way FBI is installed to the console.
Let me know where you got to and I'd be more than happy to assist. I highly suggest stopping for now and let me get a grasp on what you've done and where you are now.