RE: Fairings at the wing root
Interesting ideas, all.
There isn't going to be much room for fairings. To get a significant savings in drag from them would require they be decently large. But heck, whatever you can do is going to look kewl.
If you are interested in reducing drag, then lose the stab stiffeners. Those and the landing gear create more drag than the entire fuselage. They basically double what the fuselage creates. Oh wait, I just reread your post and you're planning that. Excellent.... Losing the flying wires is an excellent drag reduction move. Also, while you're doing the extra work, take some time and simply round the LE of the gear struts and taper the TE of same, and you'll have some drag reduction. And if drag reduction matters, then do NOT leave the wheelpants off.
You might consider placing the engine sideways. It just might give better ground handling and a cheekpiece cowling is about as low drag as possible for realistic looking cowls. Frontal area matters and sideways does that well.
You've got some good ideas. That's the beauty of this hobby. If you can think it, you can probably do it.