Sounds like you have the groundwork for an awesome short already :)

http://www.youtube.com/watch?v=Fma3hX7lz4k

Maya has the most direct pipeline to SFM

SFM was created for Valves animators who use maya so alot of the graph editor interface and hotkeys for SFM carry over to Maya.

I reccomend Maya because all you need to do to import models into maya is click the import button, it will load the .mdl with no problems. Exporting an animaiton or model is just as easy.
You can export animaitons from SFM as a dmx and load them in Maya. Since Maya has the most recent plugins you can do some pretty awesome stuff in it. You can send an animation back and fourth between SFM and Maya.

Animating in 3ds Max is probably the easiest, the gizmos are easy to grab, the keys are nice and color coded, and there are plugins for getting stuff in and out. in the old SMD format.

I don't have much experience with blender but I believe that Blender and Maya are the only two with DMX support.

No matter what you choose I will say, if animating is drawing then animating in SFM is like drawing in a bowl of pudding compared to more powerful apps.

SFM can only export animations in DMX format which currently can only be imported by Maya and Blender, Importing animaitons to SFM you need to make sure the entire shot is green in the motion editor, you cant have a rig on the animation and its better to select everything in just the "unknown" channel and import from there, make sure the dmx your importing is for the same model, unfortunately you cant import smds directly.

Portal 2 shaders might work in SFM you need to transfer the files from the 2 shader folders.

faceposing means making face flexes
Fingerposing, all you need to do is list the finger bones in your sfm_defaultanimationgroups.txt

please dont post the same topic in multiple threads

You need an IK rig for a viewmodel? Depending on how old the game is the viewmodel might have the whole skeleton already. Alternatively you can use one of the community made gordon models and apply those hands animations to it using the export/import animation menus.

Sounds like its missing bounding boxes.

Or you can use a program like virtualdub to make it an uncompressed avi to open into AE
http://virtualdub.sourceforge.net/