How to scale part of an object in 3D MAX and export to STL file?

I'm in the process of 3D printing and building the transmission, transfer case, rear axle, and drive shaft for Toyota 4WD truck shown at http://www.thingiverse.com/ericthepoolboy/designs. I found out that input shafts for the transmission and the transfer case are too small for the "clutch" and output shaft for the transmission. After scaling the "male" parts of the input shafts, I tried to export the objects to STL files but the files contain errors. I think that some faces are flipped inside out. I think that the objects need to be converted from meshes to solids. How can I fix the problems?