(if you are sure they are the right mounts) You might try putting the mounts on the car before you lower the engine in, or putting the mounts on the engine before lowering it. *either way always keep the rear mount on the car and the rear BRACKET on the engine*. btw dont worry about the other brackets yet. Just the left, right, and rear for now. Its always going to be a very tight fit, so it doesnt always mean theres something wrong.
You said that you cant get the tranny mount in, if its currently on the engine, I would put it on the car and pull the engine over, while a friend snaps the mount onto the tranny bolts.
I dont know if this helps, but I know my book says to keep the right/left mounts on the car. I couldnt get it done so I ended up putting the left mount on the engine and the right mount on the car and got it done. (still very tough)