This is the part that requires modification. To put it simply, Yamato did not make the rectangle big enough to allow the strut to lean out to the side. To fix this, make the rectangle bigger -- taking material off, using an exact-o knife, a little at a time. The second picutre shows one half of the part in question with material removed compared to the other half as it came from Yamato.
Note, if you find that you took off too much (the landing gear leans too far over), don't worry, because the wheel axle will make contact with the landing gear door, preventing too much outward movement.