how does the DoJ know what percentage of ANYTHING is going through it
That's an easy one: they make that number up, to spread FUD about it. And read the article I linked, BTW (and the source it links): the number in question has been easily disproved, with a relatively simple analysis of hidden services' hostnames resolution. Tor is not the USA's tool - it is an open source, publicly available software that was originally financed by part of the US government, period.
I realize all the Snowden revelations have made lots of people a bit paranoid (which is a good thing, mostly); but the fact is, it is extremely unlikely that tor is compromised in any serious way. Barring human error, tor works, mostly - there are some attacks possible, and there are demonstrated attempts by the NSA and others to compromise it (with some extremely limited results, both in their scope and in their duration); however, I have not seen any shred of evidence suggesting that it has been compromised in any serious way. This growing meme that "tor is broken for good", and the larger one that "if it's connected to a network, it's accessible by the NSA" is simply bullshit.
The thing is, in all likelihood, tor works. GPG works. If you encrypt something with GPG and the key is not available to them, even the most powerful security agency on the planet will not be able to read it. The advances both in basic mathematics and/or computing required to break those are so extreme that it would be very, very hard to hide it. And nothing in the Snowden leaks has suggested that those have been broken - quite the contrary, in fact, since several of the revealed documents suggest that tor and the growing encryption usage are a serious problem to those agencies.
That doesn't mean that it'll stay that way, mind; personally, I think that some sort of quantum computing might be in reach of those same agencies in a few years (and they are dumping and storing all the encrypted, non-breakable traffic they can in the meantime, I imagine waiting for this day) - and even that personal opinion will seem paranoid and far fetched to most experts in the field. But in the meantime, the most likely hypothesis is simply that those encryption algorithms and protocols are still secure. If you have any shred of evidence that is not the case, please link those - I'd genuinely appreciate it.
And finally, about Ulbricht and the other dark net markets taken down more recently: all of those have been clearly linked to human error, from corroborating testimonies from several parties. So sure, you can believe that this is entirely parallel construction, and you can also believe that Obama and most of the five eyes countries are bitching about encryption more and more to present a plausible deniability front while decrypting everything in the background; but right now, once again, there's nothing public even hinting at that.
later replicated by Toshiba
It's actually Toyota (and makes a lot more sense) - my bad.
But the "inventor" hooked up the meter, no?
No. The entire experiment was setup by the researchers themselves; the lab has no connection to Rossi, and none of the equipment came or was set-up by him. His only implication was to be here for the initial "fuel" insertion and the ash retrieval at the end, while being monitored (though that's more than enough to be suspicious of the alleged transmutation and suspect some sort of swap - still, it doesn't explain the excess energy).
Oh, he says words which he calls an explanation, but they fly in the face of already-understood theory, and he offers no explanations about why already-understood theory is wrong.
Agreed on this - it should be noted, though, that Rossi is not the only one that claims excess energy and transmutation using these kinds of mechanisms; look up for example the MIT NANOR devide (a small scale device that put out excess energy for more than one month straight), or the Mitsubishi transmutation claims in similar devices (later replicated by Toshiba). There are also other companies claiming similar things (Brillouin for one).
If this thing works (and that's obviously a big if), then I'd suspect Rossi discovered this mostly by accident, and that he has no precise idea himself of how it actually produces energy. IIRC, the few initial theories proposed are based on the idea of nano-scale lattices with trapped hydrogen inside; combined with some sort of excitation (EM usually, although not the only one that apparently produced some results) allowing somehow for the Coulomb barrier to be overcome at those scales and for a limited-scale, radiation-less (how ?) fusion to occur.
This is of course all pretty impossible given our current understanding of physics so if it does work somehow, it's wonderful news, even if it cannot be harnessed for energy; because it might lead to new, exciting physics.
No amount of careful planning will ever replace dumb luck.