Nathan - that sounds like a very interesting project. I'll try to help as I can. I'm glad that you've found OpenVSP and VSPAERO to be useful.
What do you mean the API does not have GUI capability? I just looked at the stuff bundled with the 3.41.2 Windows download and the files were all there. In order to load the OpenVSP API with certain options enabled (such as the GUI), you need to load another package, the openvsp_options package. You'll use it something like this....
import openvsp_config
openvsp_config.LOAD_GRAPHICS = True
openvsp_config.LOAD_FACADE = True
import openvsp as vsp
What analysis inputs are you asking about? Most are not documented through the GUI. However, they do have brief documentation through the Analysis Manager via the API. I also believe there is some documentation about VSPAERO on the Wiki and also the VSP Ground School. If you have a specific request, I may be able to point you in the right direction.
If you are just doing pitch trim analysis, I suggest you run in -pitch mode instead of -stab mode. It will run fewer cases -- just those needed to get the CLalpha and CMalpha derivatives. If that doesn't run control surface deflections (it might not), then I suggest you just run three cases manually -- one at baseline alpha, deltae, one at perturbed alpha, baseline delta, and one at baseline alpha, perturbed delta (start with 1 degree perturbations). Then you can finite-difference these cases to estimate your own derivatives and do your trim solution.
Running VSPAERO through the API includes the option 'RedirectFile' which you can set to '' (empty string) to silence most output. It will still echo the reference quantities. That is a bug that has been fixed going forward.
Don't worry about FOpt.
There are a ton of changes to VSPAERO and OpenVSP's interaction with it that have been building up for about two years. These will hopefully be released in the next six weeks or so. The first release will likely be some sort of Beta release as I expect the transition to the new stuff to be bumpier than our normal upgrade process.
Among other things, the new version will integrate a totally re-written adjoint capability. This will make stability derivatives much faster and more accurate. It will also enable built-in modes to take advantage of the adjoint -- these will come later in the year, but I expect us to integrate an optimization tool and also a trim tool sometime this year.
Understanding the demands on your time and how much OpenVSP / VSPAERO is going to be changing going forward, I suggest you focus on solving your immediate problems for your design team.
I can't recommend you invest a lot of time building something elaborate beyond that at this time. Hopefully we'll get the new stuff sorted and released quickly -- which will allow you to accomplish your goals better and easier than before.
Rob