If you're pro with 3ds Max, then you also know how to animate, right? Anyway, animations need to be exported to .smd files, just as the mesh needs a .smd file for itself. Then you need to compile these .smd files to a .mdl file, using a .qc file that holds the instructions for this process. I'd say, decompile a few HL models to see how this works.
As for changing damage values and such, that requires coding and doesn't have anything to do with modelling...