Do USA-based miners need to register with FinCEN? As seen in recent news, FinCEN has issued a statement on its classification of virtual currencies: http://www.fincen.gov/statutes_regs/guidance/html/FIN-2013-G001.html

Hypothetically suppose I mine BTC and sell it on MtGox for USD. Do I need to register with FinCEN as a Money Transmitter(MT)? My interpretation of the above document indicates yes, I do; but I could also see MtGox (which is registered with FinCEN) maintaining my regulatory compliance, via proxy.
No, the fincen guidance you posted has it in plain english that you do not. A miner is simply a user.

 c. De-Centralized Virtual Currencies

        A final type of convertible virtual currency activity involves a 
de-centralized convertible virtual currency (1) that has no central 
repository and no single administrator, and (2) that persons may obtain 
by their own computing or manufacturing effort.

        A person that creates units of this convertible virtual currency and 
uses it to purchase real or virtual goods and services is a user of the 
convertible virtual currency and not subject to regulation as a money transmitter. 
By contrast, a person that creates units of convertible virtual currency and sells
those units to another person for real currency or its equivalent is 
engaged in transmission to another location and is a money transmitter....


On the exchange you are buying/selling bitcoins. The exchange carries the burden of giving you legal tender or a different cryptocurrency. The exchange carries the burden of regulation, according to the FinCen regulations. In the US, the equivalent of real currency is only treasury bonds.

Also, Fincen regulations only take affect at certain dollar amounts, if you feel you need to be concerned about them.

You can also try to get even further clarification from the Treasury yourself, because on this matter it doesn't matter what kind of legal counsel you ask, nobody knows all the semantics until an issue comes up that is actually decided in the courts.