Protege5 2.0 shift problems

Hi guys! I am new to the forums and I feel like I may have a doozy here for you. I own an 02 protege5 hatchback 2.0 and I had an engine swap done on the vehicle because the timing chain had snapped. Once the new motor was put in, the car shifts very hard almost as if the motor and transmission is going to fall out of the vehicle and even once i am doing 60 just cruising it wants to fall out of gear and shifts back into gear very hard. But if I shift all the way down to 1 at a complete stop and shift the vehicle myself between 1st 2nd and then into D it shifts very smoothly and runs pretty smoothly. But even after getting it into drive if I need to punch it to pass someone it clunks very hard. Also my speedometer bounces all over the place as I am accelerating but sits completely still at 60.
 
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