RE: Phoenix Extra 330S 60-90 Size
Stevo,
Seems to me you are correct that it is a CG issue with the plane flying progressively worse as the tank empties.
However, remember that the elevator trim was set when the plane was flying with a full tank. Did you give it down trim to maintain level flight as the tank emptied? Without changing elevator trim, does the the plane fly straight and level at a high-ish throttle setting with a low fuel level?
Getting the tank on (or at least closer to) CG will help. If you could find a flat 14 oz tank and put it on CG and use a Perry VP-30 regulator, that would eliminate the CG question.
Might or might not have the wing incidence issue (it flew fine with the previous engine?), but you don't want to start messing with that until the CG problem is sorted out.