I figured out how to checked a modified secret sector to prevent use on an a9lh system (which would brick on either n3ds or o3ds, can't remember which). I'm also creating a few emergency repair scripts in case the boot9strap install fails from godmode9. One will attempt to copy the firm1.bin and firm0.bin backed up before the install attempted, and another two that will pull native firm from NCCH in ctrnand and use that to replace firm0 and firm1. That way you won't leave someones console as a brick until you can get to a computer if something were to go wrong.
Also I found a fork of godmode9 by
@AnalogMan that adds commands for SD mounting and unmounting, meaning I can now have one script install boot9strap, copy contents from SD to ramdrive, unmount and remount then copy from ramdrive to SD. Seems it's already getting pulled for the next release.
At that point the only real change I could possibly make to make the process faster would be getting dspfirm.cdc from godmode9. Currently need two scripts, one for the setup and the finalization script to do things like removing useless files, replacing the dspfirm.cdc dumping homebrew with the standard homebrew launcher, and copying luma. But if I could dump the dspfirm from godmode9 I could put everything into a single script.
With what I currently have I've gotten it down to 2:13.