Your questions are more dependent on how you will do this. A few of the things you ask are covered in the updated tutorial (sig below). I only know how (basically at that) to mess with the Module System.
You can delete all the weapons, but then you would have to look to where they are referenced. Quickest (and painful) way is to remove them and then compile. You'll get errors stating that the items are not defined. There will be quite a few (as troops are assigned weapons, weapons are assigned to the player when he selects starter character questions, and tournaments give specific blunt weapons). But you will eventually find where all the weapons are referenced and be able to remove them. Of course in specific instances (such as the tournaments) you may want to have some weapons to sub in, if you still use those missions, etc. This goes the same for troops and parties, as they are also referenced. Best to just leave them and make others. You could always add the itp_unique flag to the items you don't want to see in stores.
Changing the names of anything is easy. Just look at the tuple definition at the top of the module file (such as module_parties.py) which will tell you want part of the tuple defines the object's name.
If you want, you can edit/add new face DDS files to get different looking face textures. You can also play around with the vertices of the head objects to get a bit of difference too, but I wouldn't play too much with that. I'm just a beginner in this area myself. Hairstyles are meshes (check both the hair and beard dds files) and can be created/edited like other non-animated meshes. I think the skins.py file holds where they are added and the color ranges for each face type.
Yes, you can turn on the in game editor (configuration from the main M&B start up window). Make sure you have windowed mode turned on. More on this is in the updated tutorial. Mind you it takes quite some time to get used to the in game editor. There is a help menu in it.