Dave,
I had a friend visit me yesterday with his almost finished MB339. There seem to be some problems with the trusttube, it seems like it is too short (a few cm's), and the angle of it is off. The former in the back directs the end of the tube down into the fuse at the back, it seems like it it must be raised all the way up to the elevator wingtube, and even that might not be enough for it to clear the fuse at the back.
Have you tried to see how your thrusttube fits ?