Rough Shifting Long term effects?

[SpeedyYaris]

Hello i have a Yaris manual and I just changed the transmission fluid... It ALWAYS shifts HORRIBLE the first 5 minutes of driving in the morning... The car jerks very hard and shakes violently And then after about 5 min its back to normal and shifts very smooth... I thought changing the transmission fluid would help but it didnt.. I got it changed at Toyota.. IM just wondering if I am damaging the transmission at all and how should i go about this rough shifting in the morning?? should i just Keep the clutch in for a long time so i can make it smooth as possible?? Am i damaging the engine at all? thanks in advance. I do have about 70k on the car on original clutch.. Maybe the clutch is bad??