Hi Tugrul,
The JTAG pins cannot be used as GPIO pins. They are for core diagnostics communications only, and do not connect to any higher level processor functions.
I would probably recommend that you could use EIM_OE (V8) or EIM_RW (AB4). These two traces have resistor that you should be able to easily access. As long as you are not using them for VGA output, you can reconfigure them to GPIO pins. Another choice might be to use any of the SD1 card pins. These traces can be reconfigured for GPIO use as well.
In reading your request, I do have one concern: Logic high levels will vary from GPIO pin depending on which module (EIM, PATA, SD) the pin is assigned. Voltage levels for the different modules are determined by the power applied to the NVCC_ pins. For example, on the Quick Start board, pins assigned to NANDF module will have a logic high of 1.8V, as well as pins assigned to CSI module. Most other modules will have a 3.3V logic high. If you are taking measurements to determine how a pin will act for a future hardware build, you need to make sure you are taking a measurement from a pin that will share the same module domain. Otherwise, you might find that the pin you actual use does not have the same characteristic as the one you measured.
Hope this helped,
Mark
