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On the top of the bellhousing. From the drivers point of view it is in the 11:00 o'clock position. The harness wraps around the back of the bellhousing and plugs in on the passenger side of the block near the oil sending unit.
Check the wiring from the relay to the fan motor, and check the wiring from the fuse block. Basically check all wires that supply power to the fan motor, use a volt meter. Fan Relay (behind headlight, under battery) on the 2001 GC 4.0L are a piece of ****, I change mine almost yearly. The problem is their location, a high heat area prone to the elements. I understand that 2002 and newer, the location was changed and the problem solved. Relay might close the circuit when cold or at reasonable temps, but might open a circuit when it heats up, causing the problem.
I don't know if this will help anyone, but i had a issue with my jeep running hot and check engine light coming on as well. After alot of trips to different shops - the last one found that there were two senors in the engine for the fan that need to be changed. Everyone would aways fine the one up top but not the second one. After that, have not had any other problems like it since.