Ok, have you any experience about fuselage stress analysis??
Firstly, go to nasa tech records, download and read the following reports:
NACA 998, 1135, 1202, CR-4731, TM-999, TN-687, TN-847, TN-929, TN-1098, TN-1830, TN1831, TN-1974, TN-D400, TN-D401, TN-D402, 1239
Also, you can use some ESDU methods, and also propriety manuals.
Simply put, for a pressure case on a pure cylindrical member, their is no bending moment as the whole sysytem is self balanced as a memberane tension.
Things start to get more complicated when you start introducing fames, stringers, and discontinuites of skin curvature. These systems are all still however statically determinate.
Introduction of cut-outs causes problems for the analysis and capabilites of the airfram, think back to the torsional differences between a cylindrical shape and the shame shape with a minute cut the length, think the difference is about 482 or so.
Anyway, rambling on.
As soon as you introduce the floor beam you step into a statically indetermiante structure, and decent FEM is the way forwards. Note the words "decent", because as soon as you move away from pressure cases your constraint system will be far from reality, and give crap results.
If you have a floor beam in your model you will end up with "S" curves around the intersection.
Have a read of the NACA tech notes and this will hopefully give you your answer as to the effect of the cut-outs.
Let me know if you need any help.