I have an '01 SE 4WD 5SP. The electronics are not acting properly (power windows iratic, braking intermittantly delayed, shifting chunky). I want to run some diagnostics testing, but need some help. What is the best tool to use on my Pathy, where can I find the proper set of codes and where is the ECU located.

You need an OBDII scan tool to get the codes. It conects to your car to a plug that is located under the dash, in the drivers side.
If you buy a Haynes manual for you Pathy, in the section "Emissions and engine control system", there are the trouble codes, but most of them are for electronics controls of the engine.
BTW, the ECU is located under the dash in the drivers side, but you need to take out the cover to see it, and for the year of your phaty, it won't be of any help. You need the OBDII scan tool.