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.