Most likely your geometry isn't perfect. You need your horns to be the same distance from the hinge line, same height off the control surface etc. If anything is off just a bit, then it will show significantly on 3D throws. Another solution is to mix 2 channels on a computer radio and then you can set you endpoints to match with the radio. You may not have a radio capable of this though.

Finally, beware of the reversing Y harness. I tried one once and it changed the neutral trim settings as temperature outside changed. It would raise or lower one elevator half which was not good. Others have seen the same thing