I'm getting:...
Measuring the voltage of the various microprocessor pins rarely yields any useful information. For example with a properly operating LCD program the Enable pin is almost always low (0 volts). To transfer information to or from the LCD this pin is pulsed high (5 volts) for perhaps a microsecond or so. A voltmeter will never react to this signal, you must use an oscilloscope to detect whether it is there or not.
I take it digital pins 2->9 represent portB data pins?
Digital pins 0 - 7 correspond to the Port D data pins 0 -7
Digital pins 8 - 13 correspond to the Port B data pins 0 - 5
Analog pins 0 - 5 correspond ot the Port C data pins 0 - 5
It looks like this might be your problem.
There seems to be some issue with dpins 0 and 1 unlike the other data pins; ...
Correct. These pins, which correspond to PD0 and PD1, function as RxD and TxD when the UART is in use. They are permanently connected to the USB interface on the Arduino and therefore are not totally unencumbered when the UART is not in use.
That's one of the reasons that I use a Boarduino for most of my work. When you disconnect the programming cable the USB interface is no longer connected to the microprocessor.
Don