Two small novice questions.

Number 1. How can you edit alpha values on standard game units so that they affect transparency rather than placement of team colours?

Number 2. Is it possible to remove weapons from heroes/units without editing the base model file in 3dS Max?

Thank you for your time.

here's a tutorial for the editing of alpha-channels(presuming you are using PSP or Photoshop)
if you are using Photoshop 7.0, then you will need this plug-in.

Yes, it is possible to remove weapons with alpha editing, although it will leave an open gap in the model, it can be used.