http://www.wired.com/2014/08/operation_torpedo/
This article describes the use of malware to circumvent any potential effects of Tor. It even goes as far as to explain that the operation was successful due to a misconfigured Web service. It does not, as you originally claimed, talk about "the FBI [being] able to theoretically trace a connection if they could get a tracker installed before the jump to nodes". It also does not talk about exploiting any vulnerabilities in Tor itself - rather, it reaffirms the point that Tor does not guarantee anonymity or security.
http://www.forbes.com/sites/kashmirhill/2014/11/07/how-did-law-enforcement-break-tor/
And this article explains that it would be possible to trace connections if you happened to control a significant portion of the Tor network. Exactly as I claimed:
To the best understanding of experts in the field (NSA included, at least at the time of Snowden's leaks), your best shot at correlating Tor users to exit node activity is a timing attack or achieving control of an entire circuit.
I use TOR daily and it auto-updates since that is how to foil the feds at this point.
There is nothing in Tor's code that would in any way facilitate an automatic update. In fact,
one of your links explicitly states that Tor developers asked users to update their software - something that would be completely unnecessary if Tor did auto-update.
Also, it's Tor, not TOR.
Maybe you should read about correct downloading and usage of TOR.
Perhaps - if there's anything in particular that you think I should read, please post it here so I can access it.
That said, I probably have a better understanding of how Tor works than the average user. My involvement in the project might not be significant, but at least I can say with confidence that I've worked with Tor's codebase before. There is a lot I still don't understand, but deploying and using (parts of) a Tor network is not exactly arcane knowledge.
If used correctly, even your ISP will not know what browser you are using to connect to their network.
This claim doesn't even make sense. Using Tor will do nothing to conceal your Web browser, and concealing your Web browser is hardly difficult in the first place. That said, doing so would be
a very bad idea. If anonymity is what you're after, you want for your browser to blend in the crowd,
not stand out from all others by concealing its identity.