You can do it. It's a lot of work, but it can be done.
Do you mean the an actual transmission isn't coming off, or maybe the the outputput shaft?
On this guide, what step are you exactly on?
http://evomoto.com/tech_info.php?tec...f01d07f1f29a45
Were you able to disengauge the throw out bearing from the pressure plate?
Did you get the three mounts and all the bolts on the tranny?