Make sure the engine is high enough for the studs in the engine mounts to clear the crossmember. When I pulled one I brought the engine and trans up then just put a bit of pressure on the trans with a jack.
It is possible that they are stuck together with a bit of corrosion. Once you make sure its high enough you can insert a small prybar into any gap you have and use it to push the engine away from the transmission.
Do I need to loosen the motor mounts? If so, I did not do that yet...... I'll also try penetrating fluid overnight.