FINAL UPDATE: After three attempts at trying to repair all the problems with the engine replacement and keeping the car for a total of three weeks to try to solve these problems, the chief mechanic kept saying, "It runs great!" The engine still ran rough, there was a loud rattle in the dash when in drive at idle and the engine would surge at times at highway speeds. And the check engine light was now on, so it failed the state inspection.
I decided to take the car to another auto shop and they found a few things:
One leaking injector - gas leaking on engine Injector O-rings had not been replaced Throttle cable not connected properly - mounting bolt broken Negative battery cable not attached properly to ground Numerous cracked and rotten air hoses had not been replaced
Yet another repair cost. This time $850. At least the car is running good now. This second auto shop took four days to find all the problems. The guys who replaced the engine took three weeks and never found any of the above problems... "Uh, it runs great! Yeah, runs great..! No problems!"
Lesson learned... Do your research on auto shops before getting any major repairs done. Or, better yet, don't replace the engine - just buy a new car... Happy Driving...