Your very brave ! Which bearing are you changing and how sure are you you know which one it is ? Probably better to get another box, I have a good MKI box as a spare.
The bit you say that has been welded is normal. According to the Factory Manual you don't need to remove the shift linkage to open the case. The nut you have taken off should have a C clip on the other side. The manual states with the box standing up remove all the bolts on the case the lightly tap the rear extension which is on the bottom side to the linkage and it should just slip off. Just a hint but make sure its not in gear.