My wing roots did not fit either. Got them to line up as best I could with the top surface and then made up the difference with lightweight filler on top of the wing sheeting. Don't look to closly at the underside though !!!! Make sure if you take this route that you do not change the wing incidence though.
In answer to the question from Pete S-RCU about the tailpipe. I used the design that was explained in RCJI in the artical by John Wright. It was written around the Wren 54 but gave dimensions for other motors as well. I just scaled up the dimensions to suit the AMT Mercury. I did make a sliding mount so that I could adjust the distance from the motor to the mouth of the pipe and found that it did make a difference to the thrust. Thrust is now up on a bare motor...and it sounds good as well.

John