How can I calculate the speed gain from using multiple STC modifications together?
Not practically speaking no.  With sufficient engineering data you could perform calculations to come up with a model for what the additive effects would be of the various modifications.  

The problem with the aerodynamics to horsepower relationship is that almost all of the basic calculations have exponents.  So a mod that gives you 5 knots over a given 'stock' airspeed will not give you close to the same number at a different higher base airspeed.  So with three 5kt estimated improvements you end up with maybe 5 knots for first mod, 3kt for 2nd, and perhaps 1tk for the 3rd.  Add to that the complexity of really subtle interactions in aerodynamics could mean that one mod may make the other 2 yield no differences in cruise.

Take for example a TBM850 which cruises 300mph on maybe 800hp vs a Cessna 210 at under 200 mph on 300hp vs a piper cub going 100mph on 75hp.  

Not apples to apples, but to give a sense of the scale these effects have.