KiloB,
1.The nose-up pitching moment due to a low thrust line has no direct effect on induced drag since this is proportional to lift-squared. However it will affect the distribution of lift between wing and tailplane, increasing tail lift, decreasing wing lift (in steady cruise the sum equals weight). I have no ideaas to which wins, or if the effect is significantin the first place. Best to ask an experienced performance engineer.
2.While the vertical position of the CG has zero effect on this phenomenum, it clearly can in a dynamic situation with sudden change in thrust alone. For this one best find a handling exppert or simulator engineer.