John,
While some experts can make changes to .mdl files my first piece of advice is to not make any changes at all, there is no need to do so and the probable outcome is a screwed up .mdl.
I often open them in Notepad to look for:
1. Textures I do not want. This usually happens when I have copied over parts from other projects to save time and have not removed the associated textures. Frequently, I can find the same texture on the current model, but with a different name. Then it is just a question of working out which part has the wrong texture name and fixing the issue. Sounds easy, but it usually involves an intelligent guess or a dumb laborious search through the .X file.
The texture entries are at the top of the .mdl files and are easily seen since they are in ASCII coded text. FS is very unhappy when it can not find a texture specified in the .mdl file
2. Modeldef visibility or animation entries that do not seem to be working. These are near the end of the file. Best to search in Notepad for "VISL" There is a block of ASCII text that has the modeldef code for visible items and you should find that code in that region. Scrolling down from there you will find fragments of ASCII modeldef code associated with animations. Anything missing is not going to work in FS
3 Attachment points that do not seem to be there. This section is usually at the end of the file.
Between these sections is, for me, meaningless binary junk.
Basically, look, but do not change
The SDK is tough going, but the place to look at first when confused. I am frequently confused, but every now and then I find the answer in the SDK.
My second advice is to search the SDk and this site when you have an issue. There are threads for probably everything you wondered about but were afraid to ask. The points made are a lot easier to understand then the SDK explanations.
In summary, do not try to edit the .mdl file, but sometimes it is worth looking at the sections when your model does not behave the way it should.Then ask
Roy