I've not found much info specific to TJ's so I'm going to post what I've done. Though people should note that I'm new to HHO and mostly stumbling around.
My TJ is a '99, with a 6 cylinder, 4.0L engine. 135,000 miles. It has a Borla high-flow header (which replaced the crappy stock exhaust manifold when it cracked), but the rest of the exhaust system is stock. There are no other engine mods or alterations.
I installed a 2-cell HHO system, using the Water4Gas design. I spliced the positive lead into the the cigarette lighter's light-blue lead behind the dash board. I could not find any suitable wires inside the engine compartment (and boy did I look!) After installation, the cells were drawing 12+ volts (more like 13, but I have an analog meter), across the pair, and producing very actively.
I plugged the hose into an unused vacuum port on the side of the intake manifold, directly below the throttle body. This is very convenient!
The cells are 1 qt each, and currently using 4 tsp. of baking soda. This might be a bit much. I'll monitor the temperature of the cells and adjust accordingly.
All this I did today. No EFIE installed yet. I've ordered one, but will run the car without it for at least one full tank of gas to get get an MPG reading.