How is the timing and engine air flow adjusted?

The performance of my Toyota changed after the 90,000 mile service. I noticed initially that the engine had to turn over more to start and that the rpms were reduced.  On the highway and in town, my milage was also reduced.  The vehicle did not seem to have the zip anymore either.
I questioned the dealership repeated when coming back for oil changes but they always claimed only to have replaced the spark plugs. I had the vehicle checked out at another dealership and everything was in specifications.
Last October I drove to western Colorado and could not drive more than 50 mph in the mountains.  I had purchased the vehicle in Idaho and never had any power problems driving at high elevations before.  Upon returning to the midwest, I had the dealership check the vehicle again with the same results.  
I want to know what could have been done to change the timing (rpms) or the airflow to decrease the performance and still have the vehicle appear to be in specs.  
No one has been able to correct the problem and the dealerships have not asked Toyota customer support for assistance in fixing it.  What`s to be done?