How much current can the +5V pins supply on the ANALOG INPUTS and DIGITAL IN/OUT headers?
The total combined current that can be supplied from all 16 Analog and 18 Digital +5V header pins is 1 Amp.
Given the fact each analog input signal on the Robot Controler passes through a 1K Ohm resistor in series with the load the maximum current to the Analog to Digital Converter is 5mA. Therefore, why is it necessary to use only 100K Ohm potentiometers and are there any unintended consequences of using a different value potentiometer?
You are not limited to 100K pots on the RC unit. We have updated the 2005 RC Reference Guide to reflect this change.
Can you use a 5K joystick on the robot controller or will it damage the OI? If you can will you be limited in the range of the inputs?
Yes you can use a 5K joystick on the Robot controller, see the Reference Guide (http://www.ifirobotics.com/docs/rc-ref-guide-01-31-2005.pdf). The pots you use on the RC will not affect the OI.