computer not reading right, had manifold flex pipe replaced, tune up

What is your question?

mechanic put in an upper portion manifold pipe where the flex pipe is, then he did spark plugs, wires whichinvolved taking the car literally apart to get to back plugs. When all said and done computer not reading right, throttle no power, he replaced throttle sensor, computer still reads throttle sensory and reading mass air flow, etc... Never had problem with this before, was this all caused by mechanic doing this work? how much is a computer going to run me to flash it at a dealer or if it has to be replaced, gas is not reading right either smells like too rich and car smells like burning when running now..