If you've got a bunch of iso files on your usb drive, then it should be easy to open the iso and add or edit a few files, I'm pretty sure Archive Manager (for Gnome) can do it just like a .tar.gz or other archive, if you know what files to add/edit.
But if you've "written" the iso to it's own partition on your usb drive, then it's probably in a read-only cd format (iso9660?), so you'd have to find & edit the original iso file & then write it. Or, my favourite, add a "personal" partition to your usb drive and save a few config files (network settings, config files in home, etc), then after booting the live Kali mount your "personal" partition & copy over the config files. Write a bash script to copy them & kill/restart any services that need to read the new config too. A logout/login may be required? But NOT a reboot, just like any live linux all system files (in overlay/tmpfs) will be lost at shutdown/reboot.
Increase system read speed A LOT (but boot slower)
If you've got about an extra gig of RAM, and if Kali supports it (most Debian-based distros do) use the toram
boot option to copy all the system files to RAM. Then any reads/write to the "system files" (basically everything in /
that's not on a physical drive) will be at RAM/tmpfs speeds, probably 2GB to 10GB a second.