Measure other aspects of the car to determine wether its a bannana or not.
If its straight just loosen the mount bolts(incl box), line it up and lock em back up. You could also then mark them up for easy referance next time the engine or box is out......normally about a week or so after it gets on the road.
ive done the front engine mounts and got about 10mm! are the gearbox mount adjustable side to side? i know you can slide them back and forth but didint know about side to side?