Yes care must be exercised in using other designs for comparison as
well. I would take some of the more reputable designs. There are
certainly some very poor designs that are quite popular and so the
popularity of the design is not a measure of the goodness of the
engineering. However I think if a homebuilder exercises with care and
takes appropriate advice on some details then they stand a much better
chance of designing a successful homebuilt using this method than by
trying to do the analysis from first principles.

OK WRT aerodynamic software. I use the CMARC/PSW code from Aerologic
(Peter Garrison). This is a linear panel code and quite suitable for
what you need. Not cheap but probably the entry level aerodynamic
software if you want build a complete 3D model of the airplane. It is
not that easy to use and will realistically take you a year or part
time effort to learn properly and do the analysis on your airplane.
The support provided by Peter and Dave Pinella is excellant and I
would recommend this program. However I would also buy a copy of Katz
"Low Speed Aerodynamics" to accompany this program to help you
understand the theory and limitations of panel methods.

A simpler approach may be a Vortex lattice code. This is a cheaper
option but only allows a 2D planar model of the configuration. I use
the NASA VLM code. You may be able to find a source of this on the web
for download.

If it is aifoils you are interested in then use XFOIL. You can find
that free on the web. I use that and with care it is reliable for most
cases. ONce again though I would urge you to analyse a lot of airfoils
with known characteristics and learn the pitfalls of the code before
you use it to develop new sections.

Unfortunately there is no cheap FEA software that is any good. Entry
level is realistically in the range of $4000 USD. There are cheaper
codes though. It really depends on what you need to do and the sorts
of structure that you want to analysis. Give me more details and I can
advise further. I have used (and routinely use) a range of FEA codes.

WRT the X-Pilot program. I am not familar with it but it sounds more
like a flight simulation package. There are a number of such programs
around. Any flight simulation package that is worth anything will
require the input of a set of aerodynamic derivates for the aircraft.
This is not something that an amateur designer will be capable of
calculating with any accuracy. I think I can fairly safely say that
this is the domain of the professional - even professional engineers
stuggle with this. However if you want to try then get yourself a copy
of the USAF Stability and COntrol DATCOM and the relevant ESDU data
sheets as a starting point.

OK final comment. When using any software it is important to spend a
lot of time running it on problems with known results before you use
it to design something new. This helps you understand how to run it,
the pitfalls and helps teach how to interprete the output data. I
cannot emphasis this enough.