RE: Having engine, wing and horiz. stab on a common centerline as opposed to having it otherwise.
Hi Karol, I applaud your project. I did a similar last winter and went through some of the thought processes you narrate. My thinking was that drag forces should be balanced on the thrust line to avoid drag induced pitch. The three biggies are stabs, wing and undercarriage. In my case, I laid the horizontal sheet stab as one would do on an inverted stick fuselage. I guessed that the stabs would have a fair amount more drag than the undercarriage so that meant dropping the wing (by far the greatest drag factor) slightly below the engine thrust in hopes of having better drag balance. IIRC, the wing is 5/8" below thrust line and the horizontal stab is 1.75" above.
I don't know that there are any magic numbers but for good flight manners... some thought might help. An example of poor would be a Spacewalker I built. The engine is high, and it has a large low wing and center stab. That means that the big three drag factors are all well below the engine thrust line and considerable lever arm on the high drag of the wing. It was no surprise that the plane required a lot of up trim even though engine, stab and wing were all carefully set zero. Ultimately, I had to adjust the wing incidence positive to get the power on/off trims into alignment.
I considered my project a great success as the plane required only two clicks of down trim and no roll trim on maiden. If the wing had been left on thrust center line where first drawn... no doubt more down trim would have been needed. Offsetting it 5/8" down from thrust line countered most of the stab drag.
Finally, the project was a real thrill beyond any previous build. Part of that was because the plane was designed around what tickled my gizzard the most, it was my creation. And.... it was my responsibility to ensure it would be a success and that forced a lot of thought and effort beyond what one normally puts into a kit or built to another's plans.
Wishing you a lot of fun and enjoyment in your effort. I'd concluded even if it didn't fly great and perhaps turned out to be the field ugly duckling the experience was worthwhile but when it looked good and flew great, the satisfaction of accomplishment was overwhelming. I love to fly the plane.
PS: I'd drop your wings to about 1/4-3/8" below thrust line if the stab is 3/4 or so above.