Sorry I'm replying to this so late, I spent some time off the forums when this went up. Anyway, I'm a current Mountaineer and thought I'd offer some perspective.
First, let me say that it's a very nice start. I feel like a combination of your two versions would be almost perfect in my eyes.
When you say "Mountaineers =/=Coal Miners" you're only partially right. There has actually been a push to integrate mining ideas more into WVU's identity. The football team currently has a WVU miner helmet that's used like a turnover chain whenever we get an interception. There was a student petition in the middle of the season to create a black set for the Oklahoma game. We even gave this hypothetical uni a name: "Coal Rush". So a black set evoking coal would be more than welcome. You also NAILED the coal rush idea for all 4 sports, IMO. The gradient is a wonderful idea, and also well-executed.
Although I think the second attempt was largely improved, you got rid of a couple elements that I liked in the first. Firstly, the number font. The one the football team currently uses is definitely growing on the fans, and I think it would be wise to stick with it. The new one does look nice, though, and the way it copies the style of the "Flying WV" could be quite popular as well. I think the first one would work best on football and basketball, while the new one would look good on hockey and baseball.
Secondly, I like your striping on the first iteration better. Triple stripes aren't really WVU's thing, and we're trending away from white except on throwbacks (and as an outline around the Flying WV). That being said, I don't like the slanted cutoff, except when it matches the numbering.
I do think that with two alternate sets, one should be a throwback. It's your call, but I feel like the old football-over-the-state logo would work better on football's white helmets. That's just a personal preference, not necessarily one that most students would prefer.
As far as your baseball uniforms, you mentioned not being able to find a good wordmark. I'm a fan of this one, used on lots of WVU sweaters (also with blue on yellow):
Although in general I'm a fan of the primary on one lapel style for baseball uniforms, I feel that any set should still feature a couple of wordmarks. I also think that the Flying WV is a bit too square to appear big enough in this style.
On a final note, I really like the gold basketball uni, and the grey football helmet. I showed this concept to a friend of mine who is on WVU's hockey team, and he said he REALLY liked them, especially the white one.
If you actually made it to this point in my ramble, I'd like to thank you for taking my input about a month after the fact. I think you're just a couple tweaks away from perfection!