I'm not entirely sure what the door relay is--do you remember the full name/location on this one? I get that the door lock timer is disconnected, I just don't remember a door relay off the top of my head.
As level9 said, it sounds like the switched ground for the dome light is grounded somewhere it isn't supposed to be. Worst case, it's a random rub-through somewhere in the harness, but before we assume the worst, let's see if we can get a better idea for where--if it's in the harness at all.
Is the rear dome light also stuck on (with its switch in the auto position)? The front and rear dome light have a diode between them, so if the rear hatch is open, both come on, but if only the side doors are open, only the front dome comes on. Sounds like you've already taken the rear hatch switch out of the equation, and I'm assuming you taped up the spade terminal to where it's not grounding out on a bracket or something. If the switch is not the problem, and the rear dome is still on, that suggests a fault in the cargo area side of the circuit--and there ain't much else to it. Either the dome light itself is somehow shorting switched ground to constant ground, the switch wire is busted where it flexes between the hatch and the body, or the wire is cut/rubbed through/chewed through and grounding elsewhere along its run.
If the rear dome light works properly (and comes on when it's set to auto and the switch wire is grounded), then you can rule out the circuit from the diode back.
Does yours have the front footwell lights, and are those staying on, too? Those are on the same circuit as the front dome light, but they are not controlled by its switch. If turning off the front dome light turns those off too, that suggests the front dome light is somehow bridging switched to constant ground. Unplug the dome light and see if the footwell lights go out.
If it's not the cargo area circuit, and the footwell lights work as expected (or you don't have footwell lights), I would set the front dome to auto, and then unplug the few things that are on that circuit one at a time until the light goes out. I know you've replaced the door switches already, but I would still start there. IIRC they ground to the body, so you don't have to unplug them, just take the screws out and let them hang. Check what you can see of their wiring while you're at it, make sure it's not cracked or chewed. Those door dingers are probably a long shot, given they're working, but they're not too hard to get to, so unplug those too and see if that gets it. The stock keyless entry/alarm system also ties into the dome light circuit, so if that's still in there, try unplugging that too (it's the square box under the driver's seat--not the roundy one, that's the ABS). If that doesn't do it, I'd try unplugging the cluster as well.
I should note that I have not heard of any of the above components causing this problem, or dying due to a battery arc (did the guy seriously try to remove the alt with the battery still hooked up?). They're just all I can think of that's on the dome light circuit.
If all of that stuff is unplugged, and the light is still on, then, yeah, you've got some wiring to chase. Let me know if you end up there and I'll have a poke at the EL section, see if I missed something, or if there's an easy disconnect somewhere else in the circuit so you can narrow down the search area a bit more.