ORIGINAL: Jack H
Well yes it would be messing with the original '' kit design ''
People here know that I'm all for "messing with kit design." If fact, I can hardly lay off it!

My first ever RC model (built about 6 years ago) was the BUSA 40-sized eindecker and I ended up "messing it out of existence."

I didn't use the kit's fuselage, I didn't use the kit's rudder, I didn't use the kit's tail plane, I didn't use the kit's cowl, I didn't use the kit's landing gear or tail skid, and I didn't use the kit's one piece wing. I Did use the kit's wing (with ailerons) since, this being my first RC build, I wimped out on the idea of wing warping. In fact, I didn't even use the plans as I just enlarged the Nieto drawings to the scale of the kit's wings and scratch-built off those enlargements.
A lot of builders, including me at this point, might say that was a waste of a nice fun-scale kit. Why pay for a full kit, if you're only going to use 10% of it.
may even get some ''Real'' dog fighting capabilities against those S pad's
The EIII was a real "dog" of a dogfighter being outclassed in terms of maneuverability by many of the Allied aircraft that were its contemporaries. What it DID have was a forward firing machine gun that came as a surprise to a good many opponents. But it's still a classic and I love it.
shifting the motor back to conceal it deeper in cowl '' scale'' will bring the C.G. forward, providing further mechanical advantage of the full flying stab in pitch.
I'm not sure I understand you here. If you use a scale depth cowl (roughly half of the BUSA cowl) then you'll be moving the engine backwards by several inches. So you'll need to compensate by somehow getting more weight forward.