I have a 89 rs 305 5 speed, I was taking off kind of fast and there was a loud clunk when I shifted in to second now the entire transmission and shifter shakes up and down when accelerating. Anybody know what might of broke?

 

Tranny mount could be broke. A torn or separated tranny mount will allow the tranny to be lifted up by the torque arm under acceleration.
If that's your problem, I got one from the local parts store for around $10.

If that's not your problem, could be a u-joint on the drive shaft.