Shifting problem

I have a 1992 Toyota Paseo, it has 114,000+ miles on the car itself, only 60,000 miles on the motor, when the new motor was put in the car the Throttle Position Sensor was cracked. Would this have an effect on how the car shifts between third and forth gear? This is a new problem as of about a month ago. I have owned the car since August 2008 and have not had a problem with it shifting like this before, except when it is cold and not warmed up yet. When the car gets to between 35 and 40mph it starts to hesitate and car pulls foward when it is trying to shift into the next gear.