Putting the stove inside the pots will protect it from getting banged around. Things get banged up pretty bad riding on a motorcycle (falls or no falls). In fact you should wrap up those tools in something or they will eat a hole through the bottom of your bags. Tool roll or one of those simple tool bags from Ace will work. Anything metal needs to be wrapped or stuffed into a secondary bag to prevent damage to the bikes bags. My friend put a single tire iron in the bottom of his bag thinking the weight of the things above it would prevent it from shifting around too much. It wore a hole right through the bottom of the bag. No crash or anything just the metal pressed against the material with the addition of vibration.
Very interested in how the mighty xt does on this trip. I also have an xt and plan on making some extended trips on it.
Good luck on your trip.