I am not clear on your thrust line use. Some amphibian aircraft have
engines much higher than the main wings. The offset of the prop thrust
line to the main wings will affect fuel efficiency and performance -
the prop introduces more moment force pitching the aircraft down and
more elevator force is required to balance this - thus more drag on the
aircraft. Generally you will see canards engine thrust line pretty
close to the main wing level - but higher if anything, to keep the prop
clear of ground on takeoff/landing.

Correcting your problem? Reposition your engine mount so that at least
the engine thrust line is horizontally centered. I suppose you can tear
up the design more and do the vertical centering.