Ok there's probably something stupid I'm overlooking but here goes. I'm setting up a fuel cell in my 2000 XJ, I've got an e-2000 pump and I'm using the wires that went to the stock pump/sending unit. The battery has been on a slow charge for a day now and I've got 12 volts, if I use some jumper wires to connect the pump to the battery, the pump runs fine. I'm using the black wire and a blue/green wire because with the key in the "ON" position it has power, but only about 11 volts, it does not run the pump. It has power so even if these were the wrong wires I have a complete circuit and it should run right? Please help. Thanks

I don't know anything about the stock XJ system, but if the blue/green wire has 11 volts with the key on, and nothing with the key off, then perhaps there is just not enough amperage to run the pump, as if the blue and green were more of a remote command to activate a pump rather then run one.

Ok there's probably something stupid I'm overlooking but here goes. I'm setting up a fuel cell in my 2000 XJ, I've got an e-2000 pump and I'm using the wires that went to the stock pump/sending unit. The battery has been on a slow charge for a day now and I've got 12 volts, if I use some jumper wires to connect the pump to the battery, the pump runs fine. I'm using the black wire and a blue/green wire because with the key in the "ON" position it has power, but only about 11 volts, it does not run the pump. It has power so even if these were the wrong wires I have a complete circuit and it should run right? Please help. Thanks
Not real familiar with the 2000 XJ, but it's likely you are trying to drive the pump with the low fuel idiot light wire or the fuel gage wire.
You normally want a rather large red wire (though I have seen other colors), typically 12 (or 14) gage. This wire comes from the fuel pump relay. The fuel pump relay will only energize for a few seconds when the ignition is turned on, then continuously energize while cranking the motor or when the motor is running.
If yours is like earlier models it has four wires, pump, fuel level, low fuel light and ground.