Sorry the v2-v3 conversion didn't work more smoothly -- in some ways it is a miracle it works at all...
I wouldn't be too disturbed that the wake looks like not much is happening. I've found that some configurations don't show a lot of rollup.
In general, I do think your main wing sections need a bit more spanwise resolution. I would try to avoid the abrupt change in spanwise resolution between the outboard wing and the winglet by refining the outboard wing and decreasing the outboard clustering parameter.
I played with a case at 20degrees AOA. I found that you have a nearly triangular lift distribution with these airfoils, chord, and twist. I suspect you need to unload the center of the wing a good bit.
Sometimes I go with a heavy sideslip case to convince myself that the wakes are working properly. Vertical tails have a lot lower aspect ratio than most wings...
You can also run VSPAERO in 'Fixed Wake' mode to convince yourself that the wake relaxation is actually doing something. That said, for a well behaved model, I often find that the fixed wake and relaxed wake solutions are very similar.
In general, the VLM does not need LE/TE clustering. The Thick-surface mode does, but thin-surface does not. You can reduce or eliminate the LE/TE clustering if you're sticking with VLM for the most part.
If you want to model flaps with a gap and/or a fowler action, you'll have to explicitly model the flap as a separate component. There are some tricks, but it certainly complicates the model a lot.
The rudder hinge line problem is because it is located on the blended center segment of the rudder. You might try breaking the rudder into three sections - one for each wing panel that it traverses. The rudder is laid on top of the surface in U,V parameter space -- note the grid lines are constant U,V. So, when you want a straight control surface boundary in 3D space, OpenVSP has to jump through hoops to solve for the curved U,V line that does the best job. In this case, it isn't doing a good job, but if it only had to work on one part at a time, I think it would do better. Raw control surfaces are put into 'groups' that are then deflected by VSPAERO. This can be used for control mixing, flaperons, and all sorts of good stuff. You will also be able to group the three sub-rudders into a single rudder control that should work for you.
If you change the vertical tail to a transparent color, you will see that the hinge line is drawn. The hinge line is always a straight line from control surface root to tip. The angle direction indicator should be drawn perpendicular to the hinge line.
In VLM, the fuselage will not contribute to forces -- but it will contribute to moments. However, it can change the forces on the other surfaces. Your fuselage doesn't look like it is causing any problems.