RE: U-Can-Do 3d 46?
KAOS - Like someone else said, "Welcome to the UCD Thread"
I have my Elevators on a "Y" Harness too, and I did the same as you to solve the same problem. I have seen about 4 or 5 other UCD 46's and they were set up the same way. The rod just barely clears the stab on the one side on mine too, even on High Rates.
I'm not sure what to tell you on the aileron problem, so maybe someone else can help out there..............