'328P does not have JTAG.
Can use a screw shield between the Arduino stacked shield as another way to access pins.
Or use female headers stuck onto the Arduino female headers and then stack the shield as a way to have more room to clip lead onto. Saleae 16 channel logic analyzer will let you look at all the digital signals, if you know how to interpret them.
At the same time, it's pretty easy to write a sketch to manipulate single pins to see if they can be written high/low or read back high/low signals or analog levels.