I'm still confused. Did you mount boot0 and/or boot1 directly from your switch? like, using memdump, or something? And delete things directly out of your nand? hactool has NOTHING to do with getting a keys.txt, and neither does hacdiskmount. You need keys.txt to use them in the first place. Is your system ipatched, or can you use RCM? If so, you get all of your keys simply by injecting Lockpick_RCM with tegrasmashGUI or however you inject your loaders. biskeydump will also get you what you need for mounting nand dumps. If your console had FW7 or above, you need sept on your SD from Atmosphere.
Also, you need to combine your nand dump to mount it (assuming you can get your keys dumped). In windows, it's as simple as using cmd.exe and doing: copy /b file1+file2+file3 new_file (using all of the parts, of course. not including the boot0 and boot1 (iirc).
Now... if you've taken whatever "fix pack" boot0/boot1 files you grabbed and have tried to flash them to your switch, then yes, you probably bricked your switch by wiping out the real ones.