> MCLR. I have read information from various sources, with
> some suggesting pins should be grounded if not used

There's no need, and it's inadvisable, to hard ground any pin that's
not being used. Simply TRIS it to output and leave it unconnected

Plenty of good advice here

http://www.piclist.com/techref/logic/xtrapins.htm

> _MCLRE_ON

If this is in the CONFIG, connect MCLR to Vdd. With a 10k resistor
if you want to reset the PIC manually

Or change it to _MCLR_OFF. This disconnects the pin from the
internal reset circuitry and allows use of the pin as GP3

> Is there anything I can add to protect the chip from unwanted negative
> voltage?

The signal line(s) will be protected from the PC port by the MAX.
0.04V difference between points on a ground line isn't much of a
concern in this situation. The danger point for I/O is -0.6V, which is
when the internal protection diodes will start conducting. A simple
solution is to add a Schottky (A to Vss, K to pin). This will start
conducting at 0.3V
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