I just checked here on mine, and the click is following tempo as expected, and the Tempest is syncing just fine with itself and external hardware. It's been a long time since I did any troubleshooting on the Tempest, but the last I recall someone having an issue with the click falling out of sync with the bar counter, it was due to the default "initialized" beat being cleared when the flash drive was formatted.
Did you format the flash drive? If so, you will need to save a new initialized beat file via the debug menu. To do so, set up a beat with the default sounds and time signature you prefer. Hold both SHIFT buttons and press the SYSTEM button. Navigate to the SAVE NEW INIT BEAT menu item and select it. press the left most soft button below the Tempest's screen to save the current beat as the new initialized beat.
If that doesn't work, make sure that both your Main and Voice operating systems are current.
As for changing the length and time signature of your beats, it took me about 30 seconds to find that in the manual just now (wink).
Cheers!