adjust the clutch, if the clutch cable is loose then when you push the clutch in you wont push it in enough, basically think of it like trying to shift when the clutch is in half way~ its hard to do
thats the first step. Get upside down facing upwards under the drivers dash. Put a hand on the clutch quadrant (above the gas petal) and use the other to push the clutch in all the way. Hold the quadrant as you ease out on the clutch. Let the quadrant rotate just hold tension against its rotation. It will "click" to take up slack. Do this about 3 times until the clutch petal is FIRM at the top. Test it by driving holding your foot on the gas at 45mph and ease in the clutch holding the gas steady. If you push it in a half an inch before the rpms start to climb thats the sweet spot, you want at least a half an inch of petal before the slip of the rpms (they start to climb)
Try this before thinking the trans is done, but... if this helps and it still shifts bad... then it may have caused the issue. Hope it helps.