I've been through this before on the W115/114 and it can be tough even with a perfect subframe. One car I worked on had an accident damaged subframe with a replacement trailing arm and the differential holes were compressed and very tight. The differential had to be pried out.

When the car is on jack stands and the differential is removed the springs push the rear of the subframe toward the trunk floor. If you lower the car to the ground without the differential (don't it will damage the subframe bushings) the rear of the subframe will move toward the ground quite a bit. This seems counter intuitive but that's what happens. Try jacking the trailing arms until the subframe assumes the normal position. Be careful as this tends to lift the car off the jack stands.

If you're trying to install the differential with the rear mount attached to the differential cover (don't it's much harder) it will be impossible without jacking the arms. It can be done with the cover on and the axles in place but it's awkward.

The holes are precision made and very tight. With the differential and subframe out of the car it's still a bit difficult. You really need to bring it up straight. Tying to get one stud in first doesn't work and pushing hard on the diff just pushes the subframe to the trunk floor.

Once you jack the trailing arms you can put a block between the subframe and the trunk floor to help keep it in position and give you something to push against.

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1969 220D 5 Speed (OM616)
1983 240D 4 Speed
1985 300D Auto 376K
1985 300D Auto 275K