I don't think you understand . "Vin " in the INPUT to the 5V REGULATOR
IT NEEDS TO BE 2 to 2.5V HIGHER THAN THE OUTPUT (5V) so that means the MINIMUM Vin is 7V to 7.5V.
The Vout (that' Vcc to you which is labeled "5V" on the board (not Vcc) should be about 5.1V dc
Adjust the pot on the buck converter up just slightly until the voltage on "Vin" is 7V. Make sure the buck converter is actually connected to "Vin " and not "5V" . Presumably you have a 2.5mm round plug plugged into the external dc power barrel jack.
If you don't have the plug , Vin is the same thing.
Your USB voltage is too low because you exceeded the 500mA maximum load for the USB. You have over-loaded it. Disconnect the buck converter , plug in the USB with the voltmeter connected to "5V" pin and start disconnect things , starting with the lcd shield
(with the power off of course) . Disconnect your loads , one by one and then plug in the USB and measure the 5V pin again. You will see the voltage increase , the more load you remove. It's not rocket science.