The problem sounds like you are not pulling it far enough out to drop the whole thing. The output shaft is long (I am pretty sure it almost touches the crank) which means it might still be partially engaged with only 3" of separation.

Along with the trans mount over by the driver wheel well there is also a damper/bobble strut on the backside near the differential housing that connects to the K frame. When you unbolt the trans mounts from the frame, also go ahead and unbolt them from the trans, completely removing them. This might give you a little extra clearance to separate the trans and engine.

If you still cannot get it out, I would just try unbolting the pressure plate from the flywheel since you said you had 3"s of space.