Chopperguy,
I have the same situation with the gear doors on my h9 p-51 also. It looks to me like a design oversight on the stackup dimension when thr gear is retracted. My bird flying by, the're just about invisible, you are looking at all the beauty of this plane, you don't see them. Trust me, you won't experience any performance issues. Your right, the plane looks lame with them removed. As for the steel wing bolts, I don't know what all the hoopla is about, they have something like 400lbs. of sheer strengh each. The wood around them would fail way before the bolts would. Thre is no c.g. issues with the steel ones either. I personally was impressed that h9 would spend a little more on the steel vs the nylon ones. I have a custom stainless steel exhaust on my plane, and I have a hanger and end of the exhaust hanging off the right side bolt, no issues.
You're gonna love this plane in the air! When taking off remember to hold constant up elevator when taxing and during the rollout, or you will experience nose overs some friends talk about.(speaking from experience.) It seems a little strange at first doing this, but you'll get use to it. Enjoy!