2004 Sequoia Limited - Immobilizer bypass repair

Recently purchased a 2004 Sequoia Limited 2WD that has some electrical issues. I had a general idea of what kinda horrors I was getting myself into, it was surrendered to a shop because the previous owner couldn’t afford the repairs they performed. So far, I can tell an aftermarket head unit and amp was hard-wired in, and then cut out before I bought it. Did some digging with the radio out, looked around behind the dash/cluster/under the steering wheel, I verified that there is an ECU immobilizer bypass installed, which allows my 1 chipless ignition key to turn the vehicle on (key also works in the door lock cylinders). I plan on getting back in to take a closer look, and some pictures if it’ll help. What I’m asking is, if I were to remove the immobilizer bypass, would it be possible to program an OEM chip key? I did watch a video on an immobilizer bypass install, just to get an idea of where to look for the black box, which might be containing the original chip key (?). My main goal is to get keyless entry/anti-theft alarm working without installing aftermarket. From my initial inspection, it didn’t look like there was already an aftermarket anti-theft installed, but I’ll check again. Also, the power door lock button on the driver side only actuates the rear hatch lock. None of the front/rear driver/passenger doors lock/unlock via the driver or passenger door lock button. The door wiring harness is chopped up (of course) to what looks like hardwiring the tweeters to the speaker wiring. Would the door lock actuator be at fault for this? Or could it be the door lock switch or Immobilizer bypass causing it? I’ve spent the past hour or so looking around here for answers and didn’t get far, so hopefully I’m not about to be referred to a past post that fixes my exact issue. Thanks for any help, I’ll try to provide pics or more information as soon as I can.