Netfabb Basic (www.netfabb.com) can load the X3DB and save it as an STL (or vice versa)
For larger models, the repair tool requires a considerable amount of time to complete.
The thin walls visualization tool has to subdivide your model into "voxels" that are each on the order of 0.1mm in size - your model ends up being more than a million voxels to process. Then the Repair tool has to do a simliar process, but (I think) that it uses voxels of 0.05mm - more than 8million to process.
Looking at your model, I would suggest:
1) fix the four flat panels in the nose cone - each of those need to be a bit thicker.
2) fix the small post in front of the cockpit - that too needs to be slightly bigger
3) ignore the reported error on the belly and the tail - those are "false positives"
4) consider making the thinnest part of the landing gear a bit thicker. Even though it passes the ThinWallsCheck, the wheels are large enough that the smallest peice there may snap.
Then, I would run the model thru cloud.netfabb.com before uploading it to Shapeways.