It sounds like someone gave you a Chilton's or similar book which is worse than useless since it gives so much incorrect information. In later models of TJs, the leak detection pump system is located up inside the passenger-side rear tub corner next to the gas tank, in a very difficult location to work on. You gain most of the access to it up through the bottom above the flap that covers the bottom. I'd expect you'll end up having to drop the tank to get to everything possibly causing the problem. And how's the gas cap? It's a common source of a leak that can stop it from passing smog.
These are out of the 2004 Mopar Factory Service Manual and Mopar Parts Manual Guide. The drawings may help show the complexity of what you're troubleshooting, especially the spaghetti on top of the gas tank. Good luck with it.
LEAK DETECTION PUMP MONITOR (IF EQUIPPED)
The leak detection assembly incorporates two pri-
mary functions: it must detect a leak in the evapora-
tive system and seal the evaporative system so the
leak detection test can be run.
The primary components within the assembly are:
A three port solenoid that activates both of the func-
tions listed above; a pump which contains a switch,
two check valves and a spring/diaphragm, a canister
vent valve (CVV) seal which contains a spring loaded
vent seal valve.
Immediately after a cold start, between predeter-
mined temperature thresholds limits, the three port
solenoid is briefly energized. This initializes the
pump by drawing air into the pump cavity and also
closes the vent seal. During non test conditions the
vent seal is held open by the pump diaphragm
assembly which pushes it open at the full travel posi-
tion. The vent seal will remain closed while the
pump is cycling due to the reed switch triggering of
the three port solenoid that prevents the diaphragm
assembly from reaching full travel. After the brief
initialization period, the solenoid is de-energized
allowing atmospheric pressure to enter the pump
cavity, thus permitting the spring to drive the dia-
phragm which forces air out of the pump cavity and
into the vent system. When the solenoid is energized
and de energized, the cycle is repeated creating flow
in typical diaphragm pump fashion. The pump is con-
trolled in 2 modes:
Pump Mode: The pump is cycled at a fixed rate to
achieve a rapid pressure build in order to shorten the
overall test length.
Test Mode: The solenoid is energized with a fixed
duration pulse. Subsequent fixed pulses occur when
the diaphragm reaches the Switch closure point.
The spring in the pump is set so that the system
will achieve an equalized pressure of about 7.5”
water. The cycle rate of pump strokes is quite rapid
as the system begins to pump up to this pressure. As
the pressure increases, the cycle rate starts to drop
off. If there is no leak in the system, the pump would
eventually stop pumping at the equalized pressure. If
there is a leak, it will continue to pump at a rate rep-
resentative of the flow characteristic of the size of the
leak. From this information we can determine if the
leak is larger than the required detection limit (cur-
rently set at .040” orifice by CARB). If a leak is
revealed during the leak test portion of the test, the
test is terminated at the end of the test mode and no
further system checks will be performed.
After passing the leak detection phase of the test,
system pressure is maintained by turning on the
LDP’s solenoid until the purge system is activated.
Purge activation in effect creates a leak. The cycle
rate is again interrogated and when it increases due
to the flow through the purge system, the leak check
portion of the diagnostic is complete.
The canister vent valve will unseal the system
after completion of the test sequence as the pump
diaphragm assembly moves to the full travel position.
Evaporative system functionality will be verified by
using the stricter evap purge flow monitor. At an
appropriate warm idle the LDP will be energized to
seal the canister vent. The purge flow will be clocked
up from some small value in an attempt to see a
shift in the 02 control system. If fuel vapor, indicated
by a shift in the 02 control, is present the test is
passed. If not, it is assumed that the purge system is
not functioning in some respect. The LDP is again
turned off and the test is ended.