when you pulled the shaft, was it still attached to the hub or did it pop from the hub as well as the gearbox?

the other option of diagnoses, based on this, is that it may have popped out of the hub side which hasn't seated properly again and this is what's caused it to be pushed further into the gearbox side

is that on the side with the intermediate shaft? because there should be a secondary shaft running along the back of the engine

there are a lot of variables though so it may require a full strip down

one more thing i've just thought of, did you change the top mount when you changed the springs? because mine was fubar when my spring broke and the bearings were all over the plce and it sounded horendous