The barometric pressure sensor, located on the top corner of the airbox under the seat, and the intake air temp sensor allow the ECU to adjust mixture for both altitude and temperature changes, albeit they both have limits and are subject to non-linearity and manufacturing variations. As you go up in altitude the absolute pressure drops so the ECU adjusts and injects less fuel to maintain AFR. The result is that with 20% less air, and fuel, the bike produces 20% less power and likely even less. Why: because the intake and exhaust tracts are designed, or tuned, as is cam timing, for air density near or at sea level. Denser air conducts sound faster than thinner air so the farther away from sea level the less in tune those systems become. The result is even greater power loss than just the change in air pressure would indicate.
The position of the air temp sensor is critical. If it gets much heat from the radiator, or engine itself, it will result in a leaner running motor. So when climbing a mountain, the engine makes less power the higher you go, has to work harder due to the grade and creates more heat for the radiator to dissipate and the engine to radiate. Slow down to drive through a town and the bike can run like crap if the temps sensor is getting heat other than from the air flow in the intake system. Even when properly placed, the air flow through the intake is so low at near idle throttle openings that the whole air cleaner gets heat soaked. (This statement is made under the supposition that the O2 sensor is not active. The O2 sensor can compensate for this heating affect so long as it remains with the scope of the O2 sensor operating range.)
As to the thump: Did the driveshaft universal joint get inspected when the bevel box was changed? A bad u-joint can bind at a given rotational position and induce a vibration into the drive system. Is the thump episodic or is it constant and rhythmic? Does it change under different loads? Test the load condition by riding the brake; does the vibration change at all? A failing torsional bearing may exhibit episodic vibration whereas a failing u-joint would be prone to rhythmic vibration.