I hope you didn't mind me asking, but to get someone to talk you though it, was a bit open ended
what can you not edit with mfw-builder, can you explain? the reason i am asking is mfw-builder as fantastic as it is, is only a gui that runs tcl scrips that simply unlock files find and replace code re-lock and save out, all from commands in the tcl's and with debug. if you or i did it the way you wish to be guided would end up with a bricked ps3, unless you can debug your pups before installing. mfw-builder can do anything you wish with a pup, its the lack of tcl's to do the job's we wish.
one more thing what are you trying to change that you think mfw-builder cant?