The easiest way to test for bad capacitors is to use an oscilloscope and look for ripple or noise on a power line.If you can't do that, just replace the power supply capacitors.
However, when you power it with the USB directly, the supply should not drop to 3.3V. When you run from the USB power, what pins are jumpered on JP4 and the power select jumpers.
OK, something is wrong. You should not see 6 V on the 5 V line.Are you near a Harbor Freight store? They typically have a digital MM for $3 on sale, $5 regular price.Or you can try reading a fresh, unused 1.5V battery.
Brand new 9v shows as ~11v read directly, and 6v again on arduino.