I must have read 100 papers which talked about subtracting the baseline but didn't tell you how to do it. Finally I stumbled on https://publiclab.org/wiki/how-to-obtain-transmittance-absorbance-spectra where they give the equations to figure transmittance and absorbance. Its just division for transmission, sample/baseline. And it works too!
This is the 900nm long pass filter I ended up using as the last order sorting filter.
I thought about putting this all in the program but I think I will do all the math and graphs in google sheets or excel. Its easier to mess with the data that way.
So at this point the software and interface are pretty much done. Next I need to make a box to test filters. It will go between the output aperture of the spectrometer and the sensor with something internally to mount the optic I will test and the ability to set the angle of the optic. Probably also figure out a way to make it so I can put the sensor in the box and movable so I can measure reluctance on angle of incidence.