Oh good....post a link to your shuttle FDM and I'll have a look at how YOU do it, as you're not posting an example of 'good practice'...
You really do walk into these things...
I actually did post a graph of the pitching moment due to elevon deflection for precisely that purpose - I'm sure you can find it reading back in the thread (hint - page 32).
So, you can see that in general there's alpha dependence, the dependence on deflection angle is non-linear and there's Mach dependence (and any FDM which doesn't have these characteristics does 'something wrong' - the question is just how badly, for instance unless you approach the transonic region Mach dependence may not matter, the moment may be rather close to linear...).
You may in general even expect that the effect of one airfoil depends on the deflection angle of another (again, question is, how much).
I suspect the most important thing right now is - understand the data you're using (disclaimer - I haven't looked at the input for the Cub), If the data is from a reputable source (say an engineering paper, a thesis,...) then you may assume the author knew what he was doing, and then you need to use the same conventions (reference areas and lengths) if you use the coefficients - you may
not use hand-waving arguments or scalings of the reference areas to 'just' change them 'to make it more realistic' - you'll just make it wrong if it differs from the source.