Manual car bucking when it needs to be shifted?

Just bought a '95 Geo Prizm, 5-speed, I had the transmission replaced, and another part like a fan or something that was closely related to the transmission. (I don't know anything about cars, by the way) I was bringing it back from the mechanic it was doing this terrible bucking or jerking so I brought it back. They replaced the fuel injection pump and did a tune up and also added some coolant and power steering fluid cause they knew I was pissed that I had to bring it back. It's still bucking, but not as bad, usually right around when it needs to be shifted at like 2500 to 3000rpm and sometimes even goes to 4000rpm. It also does it almost all the time when it's on the highway, basically when its going faster than 55. I had my dad check it out, he couldn't find anything and he drove it and said it was driving great except for the bucking. It only does it when my foot is on the gas though. The mechanic said that it was sitting on the lot for awhile and it might have bad gas, I filled the tank and put some gas additive in it to help clean it out. Only a slight difference though. Any thoughts? Remember I don't know anything about cars. Thanks.