I have the same problem on my samurai too!
When I fill the tank it reads below empty. I reset the trip odometer, and as I put a hundred or so miles on, it will then show about a half tank. After it reaches the half tank mark, it will work correctly.
I don't think it will be wires mixed up, I am betting that it is a bad ground. I am not sure, it just where I will check first. If it is not a ground, I am leaning towards the fuel tank float. I have a spare tank just incase I need parts.
I have heard if your fuel gauge is stuck on E, that is a bad ground.
If your fuel gauge is stuck on F, that is a faulty gauge.
I haven't had time to fix mine yet, but I need to.
If you get your repaired, please post back to let us know what fixed it.