Currently working on:
'Nother update: I found a work around until this can be fixed, see my post below. Essentially I have to export the meshes & animations separately because as soon as you export with an animation is messes up the bones. I can modify the animations from there separately.


HUGE UPDATE: I've fixed the problem by removing all animations (deleting keyframes in dopesheet), and exporting without them. Then the animations that came with the decompile work as long as they weren't exported with blender. My NEW problem is that I need to edit the position of the bones, and I can't do that 'cause exporting the animations doesn't work. I'm really not apt at animating, and something is happening incorrectly, but I don't know what.

EDIT: Does it have something to do with what Artfunkel says in this thread? Something about how animations cannot be bound to objects in blender?


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Update:
Okay update: When I set the compiled mdl's animation frame to 0 the model is in the, I don't know what the word is, the original position, not the default 0 animation. It's easier to just upload pictures:

This is what the frame 0 is of compiled mdl[drive.google.com]
This is what the frame 0 is supposed to be[drive.google.com]

EDIT: I made some gifs of the animations. These illustrate the problem very well:
.mdl with incorrect position[drive.google.com]
correct positions in blender before export[drive.google.com]

The animations (which may be correct or not I cannot tell) continue from the wrong position 0, and I get the wonkey animations, and model in the wrong place as shown here.[drive.google.com]

And in case anyone thinks selecting the "Legacy rotation" would help, here's what I got when I did that[drive.google.com].


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Original post:
After hours of searching for solutions to my problems I find solutions that BST has already fixed. HOWEVER, now when I export from blender using the new Goldsrc button, the bone assignments are wrong. I think this is a great depiction of my troubles[drive.google.com].

I'm trying to just learn the basics here as I'm making the weapons for the Half-Life VR mod. In this case all I did was decompile the mdl that came with HL1 using crowbar. Then I imported it into blender, fixed the UVs, and exported it.

BTW, I get the exact same thing if I use the guide that SkyNinja gives in the developer wiki here and the exact same thing again if I use this tool [github.com] that supposed to do the same thing.

One more thing, I'd like to thank the devs of this tool, it's ♥♥♥♥♥♥♥ awesome.

EDIT: With suXin's help I tried decompiling with the mdldec decomplier, and even with a new/different qc I got the same thing :(

EDIT2: Tried with the Hivehand, and I get the same mismatched bones.