I'm a bit confused, you have a '98 with a 4.6L in it? I didn't think they came that way in '98, anywhere. If so, hard to say what the PATs system is capable of (though the next generation had starter interrupt not fuel pump cutoff), but for a '98 4.0 or 5.0,
PATS only disables the injectors, not the fuel pump, though I seem to vaguely recall that someone had a European explorer that had a fuel pump cutoff circuit too, and I "thought" it was a 2nd gen Explorer but I could be wrong. I've never heard of a US market 2nd gen Explorer with fuel pump cutoff as a PATS2 function.
If it has a fuel pump cutoff there is going to be an additional module in series with the pump, near the pump, that you can find by following the wires from the pump, and completely wiring it out by jumpering around that, taking the power lead straight to the pump from where it inputs to the deactivation module.
To clarify, the theft light should blink slowly with vehicle just sitting, and may come on solid with the rest of the gauge lights when you turn the key as the bulb check for them, but then does it start to blink rapidly trying to start it? If rapid blink, that means PATS is preventing starting and as Mbrooks mentioned, there's no jumpering around that as the PCM is not energizing the fuel injectors, and you can't just jumper power to them since they have to have synchronized (timed per cylinder) on/off activation from the PCM.
If the fuel pump is also not working (easy to tell, is there pressure on the fuel rail?), then you may have two separate faults to fix, or if the theft light is blinking slow instead of fast, only a fuel pump /fuel delivery issue whether pump or wiring or relay, etc.
IMO, something like windows not working isn't really a reason not to put any money into it to fix something else, but of course it depends on how much you want to DIY. Windows are often a wiring problem and just take the time to dig into the wires and solder bad ones at the fault, almost a free repair to DIY.
It also might be stuck in 4WD which is not keeping it from rolling.
Can you elaborate? If it is the 4.0L with 4WD rather than 5.0L with AWD, the 4WD function depends on an electromagnetic clutch so if that is somehow seized in an activated position, you probably need a new or rebuilt transfer case (probably chewed up debris inside to cause that). Otherwise, what is mechanical is 4WD High vs Low. If it is stuck in low you can take the shift solenoid motor off the transfer case, manually move the transfer case back to high, manually move the shift motor to high, then put it back on, making sure the dash knob is set to high or auto. Regardless that wouldn't keep it from starting.
