Which will be prioritized when I input synchronized signals to all of USB-B, MIDI IN, CLOCK IN and DIN SYNC IN/OUT2?

Clock source set in [Sync Source] of the [Sync Common] setting category in the GLOBAL menu will be prioritized.
For details, please see the "[Sync Common] setting" in the GLOBAL menu in the Operating Instructions of this unit.

You can download the Operating Instructions from the Pioneer DJ support page
https://www.pioneerdj.com/en/support/documents/production/toraiz-squid/.