As to your fuel guage, the factory dual tank setup is a NIGHTMARE! Theres a thread here detailing how it works, but the basic setup works with the 2 tanks, a transfer pump to move fuel from the rear tank to the front tank, a sender in each tank that is ran to a balance module(it is supposed to be mounted on the frame rail near the engines lift pump) that controls the transfer pump and converts the 2 tank senders values into 1 for the guage, once the fuel level in the front tank begins to drop below around 3/4 or so, the balance module activates the transfer pump to start moving fuel from the rear tank to the front tank, if the fuel level in the front tank gets back near 7/8, it stops the transfer pump to prevent overfilling the front tank. If the balance module detects ANY abnormality in the system such as a fuel level not following what it should do like the rear tank level not dropping with the transfer pump on, the front level continuing to rise after the pump is shut off, a bad spot in the sender where it rapidly fluctuates(VERY common problem for the sender contacts to oxidize when it's allowed to sit), pretty much ANYTHING, it disables the transfer pump, and can send the guage to empty.
As to the vats, most either install the baker electronics bypass so as to eliminate the whole vats system, install a resistor in place of the sensor in the ignition switch and do a theft learn to the resistors value(if you can match the resistor in the current switch, you shouldn't have to do a relearn), or either have vats disabled in the ecm or swap in a 96 ecm without vats.
