Ok let me the first to welcome you to the forum Matt
Now lets talk about CG. For any trainer such as yours it will fly best and needs to be at 25% mac. In other words quarter chord, this is also where the spar of most (not all) trainers is located. With a straight chord untappered wing such as yours even without using the spar as a reference you can simply divide the distance from the leading to trailing edges by four and that will give you the CG you need to target.
Now to the engine. Let me congratulate you on your choice of engine, The AX line is my all time favorite. First I cannot remember if the PT 40 came with down thrust or not but if it does not for what ever reason it sure would not hurt to add a little down with some shims under the top side of the engine mount. Also from reading your post it sounds like you are flying this airplane at full throttle. Please forgive me if not but I must address this. And that is no trainer is going to fly well or at least as intended at full throttle all the time. Most will fly perfectly after takeoff and climb at around a quarter throttle.
One last thought also it sounded like you may have been recovering even from a slight dive at one point and the leading edge lifted off the saddle. This will cause the behavior you seem to have experienced at one point. Its cause is far to few rubber bands on the wing.
John
Unless your wing chord is 161/4 inchs I think your 41/8 figure for CG is to far to the rear.