Check the cruise control cable.  I had to fix one of these because I jacked
the engine while replacing the timing belt and it pulled the cable out of
its crimp.  

Another idea is the throttle position sensor, but these have been pretty
reliable on the Sonata, and shouldn't be causing anything as dramatic as
you're describing.

Beyond that, take your car to someone who has a clue.  It seems pretty
obvious that if you've spent $1000 toward fixing this problem and that
it's no better, that the place you have it has no real idea what the
problem is and intends to charge you for every guess they make.