As mentioned before, the limit is thermal derating of the main regulator. If you can keep that cold enough to not trip out, you can set the speed as high as you want.

Temperature is not available on USB. Nothing is. USB is wired straight to a UART adapter wired straight to the ASICs. If you can tag into the fan header (or the PWM testpad) it'll give you a rough idea of temperatures, within limits - it goes from 50% to 100% duty cycle between 30C and 60C.

The jumpers are a header used to program the onboard micro which handles string lockup resetting, overtemp shutdown and throttling fans based on heat. You won't need to know about it unless you are planning to write a custom firmware.

If you've got more questions, I'd try searching first. This thread and the dev thread can tell you pretty much everything, including the answers to all of today's questions so far.