Rigging the World Mesh Using Mod Tool
The weightmap file is not quite right for importing (probably because Valve Source Add-On hasn't been properly updated), so edit the file as follows.
The Valve Source Add-On for Mod Tool includes two weightmap options: Export Weightmap and Import Weightmap. These two options can save you a lot of time if your custom model is posed and positioned closely to the L4D2 survivor model it is replacing. The imported weightmap likely won't be perfect (such as lower parts of hair), but the harder-to-weight areas, such as shoulders, chest, and hips are often good enough to not need tweaking.
Convert SMD File To FBX File
Open Blender.
Delete any other meshes from Blender.
Import SMD file:
File > Import > Half-Life 2 Mesh (.SMD)
Select "Static Mesh...".
Select the smd file to import.
Click the "Import SMD..." button.
(Importing can take a while and can freeze the program while it is importing.)
Select the mesh.
Select the armature.
Export as Autodesk FBX (.fbx).
Enable the "Selected Objects" button.
Change Scale to 1. (This might need to be increased.)
Enable the "Rot X90" option.
Enable only the "Mesh" and "Armature" options in the list of export object options.
Disable the "Enable Animation" button.
Click "Export" button.
Select where to store the file.
Change the file name.
Click "Export FBX" button.
Close Blender.
Convert FBX File To Valve's Weightmap File
Open Mod Tool.
Import via Crosswalk > Import FBX.
In "Load Options", select "Add to scene" option.
In "Import Options", uncheck all the checkboxes.
In "Animation Options", uncheck all the checkboxes.
In "Special Options", only check the following checkboxes:
"Import skeleton elements as nulls"
"Keep XSI effectors"
"Set envelopes"
"Show the Warnings and Errors dialog box"
Click "OK" button.
(Two warnings about BindPose always appear for me, but they don't seem to cause any trouble.)
(Select the model/mesh and export the weightmap. Check "Export Fullnames".)
Close Mod Tool.
Edit the Valve Weightmap File
Modify the saved weightmap file using Notepad++ (or any text editor with "Find and Replace" feature):
Find "Bip01_Pelvis." (note the period at the end) and replace with "ValveBiped." (note the period at the end). (62 occurrences)
Find "Bip01_Pelvis" and change it to, "ValveBiped.Bip01_Pelvis".