The chassis member that holds the steering box is prone to rust behind the box or there might have been a minor collision in the cars past. As you've changed the box you'll know if there was any rust but not about any distortion. However, I'd undo the steering box mounting nuts and see if it will tilt a few degrees and so lift the shaft a bit. Retighten.
The sponge is just a fume/draught/noise barrier but worth replacing with a similar piece of foam. Something a bit more hardy than the original. A little silicone grease around the shaft will stop squeaks. I make them in 2 layers so that the cuts you make to fit them can be off set 90 or 180 degrees. Add a bit of glue between the layers after fitting but before you replace the clip.