I'm pretty sure that I've been bedding the pads correctly. I essentially followed the steps that you outlined.
The brakes are Shimano XT's from maybe 5-6 years back. Not exactly sure of the model. I've tried a mix of non-Shimano pads and rotors, and the latest setup is all Shimano, to see if that makes a difference. I only have a couple rides on these new pads/rotors, but I'm hoping that they will last longer so I'm trying to figure out what I need to do.