I had exactly the same problems with my project, the Horus. If you compare the avatar pic (initial concept) on the left with the current version of the aircraft on my page (www.beast.aero), a lot has changed CoG-wise. For the spar there is not so much problem as it is behind the pilot, but the point 3 cannot be avoided.I wonder if others have come up with same the problems.
1. To get the spar carry through the fuselage will severely seem to cause plane to be bigger than intended.
2. There seems to be no way to get into the cockpit if everything else seems to be nice and tight.
3. Without pilot inside the plane seems to drop to its tail albeit being a nose wheel design.
The BD-5 that you mentioned, has a sandbag that is put next to the pedals to keep it straight on the ground. In my aircraft, i am adding a retractable "bikestand" in the dorsal fin.