I had mine made (longer with braided stainless) at a local shop that also makes power steering and AC hoses. You might look and see if you have someone like that in your area.
You asked about long vs short water pump. With a long water pump you will be able to fit your fingers between the back of the water pump and the timing cover. With a short pump it will be quite close.
Dave
Fuel level senders in the fuel tank don't all work the same. Many aftermarket gas tanks use a GM 90 ohm sender. I'm not sure what the FJ fuel gauge is set up for, but it sounds like a mismatch between the sender and the gauge to me. I'm sure someone else can chime in and provide better details.