Car goes into all the gears fine with the engine not running, but when the engine is running, I cant put it into any gear. What could be the problem?

 

assuming its a hydralic tranny...it the slave cylinder pushing out the throw out bearing far enough? Has the clutch line been bled and are all the air bubbles out?

 

dont know if you changed the clutch before you dropped the engine in, but someone I know had a similar problem and he ended up putting the clutch disc in wrong, he opened it, flipped it and that was it..........check your hydro lines first before you have to drop the tranny.....check all other options first before doing that. Good luck