SOLVED: Not sure what was ajar really, but I jut disconnected and reconnected all of the electrical we interacted with, put it back together and now she's golden.
Hey people, helping a friend with his FZ6. Just finished a valve clearance check at 22k miles, during which we disconnected most of the wires (but did not remove) the tank, throttle bodies, and cooling system, although we did drain/refill the coolant.
The engine sounds fine now that it's back...