I Pulled a motor and box out of a TE 4cyl today. The car was t boned on the drivers side and has bent the CV Shaft. The CV was locked into the gearbox and wont come out. Is the box damaged?

It all depends. Impossible to say without seeing pics of the box and/or driveshaft. It could be just as simple as you don't know how to properly remove the driveshaft.

Is it the actual CV joint that is damaged or the driveshaft?

If the hit was big enough to break a driveshaft then it's likely that it could've got jammed into the gearbox. It would be a fair assumption. You may need to smash the driveshaft it from the other side of the diff/transaxle to get it to come out.

Best solution would be to try and find a gearbox that hasn't be involved in a direct accident. Surely you can find a 4cyl TE easily.

Bent shaft and jammed shaft, trow it away as it will most likely be shagged

Ended up using another one, wasn't worth the risk. Something is definitely wrong, as the passengers was easier to get out. Also upon further inspection the lower control arms were bent, and the steering rack was snapped. Goes to show how energy can transfer through a car as the car was hit right on the two drivers doors and the guard is still pretty straight.