Very similar solution. After wasting a day as you described, CC advised me to use a thin long screwdriver (found cheap one on amazon) to hold the top of bmw diff, gives more movement whilst sorting bottom bolts. Then once bottom bolts are finger tight, use the persuader knock the top bolt in (and screwdriver out).
The top bolt is held in bushes that flex as you knock the top bolt in, so with bit of force it lines up.