I think if you just mount the motor a bit higher or lower with out changing anything else it will not make much difference. If you aren't shimming the motor or mounts the thrust lines shouldn't change. If you were building some real balanced model for competition it might have some changes?

I used to LOVE kit-bashing models, this sounds like a really cool one.. Love to see pics of it as it goes along..or is finished.
I think the plane you are building is a good flier and shouldn't surprise you on the first flight.

So few people build, and very few kit bash.. many people won't post on things they haven't done..