Mine does the same in terms of having the switch in the off position turns it on Nd vice versa. Never understood that, but it works so I also never researched it or tried to fix it.
The OD light flashing sounds unusual though. Particularly because it's flashing in a pattern. It reminds me of when the ECU is put into that mode where you can read the flashing "check engine" lights to determine DTC Codes? You can reset the auto trans by disconnecting the battery(s) for about 15 minutes or so, reconnecting and taking it for a strong drive out in the open road. But it's possible their is a dodgy wire or solenoid on the actual auto trans itself that needs attention.
The port shape you're referring to is the older style M-OBD, usually found in the engine bay while the OBD2 port is usually found under the dash in the drivers footwell (if installed). You can get an adaptor that goes from M-OBD to OBD2 then use a Bluetooth dongle from there but i've never had any luck with that on my mates 1996 Prado (Petrol). The ECU just would not connect for some reason. You might be stuck with doing the old "join the 2 pins" technique for reading DTC codes. You might be able to persist with it though and work it out.