Your wing and HT are fine.
You should always start simple and build up complexity.
In this case, you should start with just the wing / tail, get that working satisfactorily and then add more.
You should start with just one or a few alphas, then add a sweep of more points if you need it.
In the new OpenVSP / VSPAERO (3.45 and newer), I recommend you use Sets to put the lifting surfaces in one Set (that will be analyzed with thin surfaces) and the fuselages in a separate Set (that will be analyzed with thick surfaces).
I suspect your core problem is something to do with the fuselage skinning.
Rob