Factory Alarm... ugh.
When I got the car it came with a remote with nothing written on it, that didn't do anything. The car didn't seem hamstrung by this though, it appeared to have a mazda branded siren in the engine bay which was switched to off.
While trying to find the issue with foglights I discovered the main unit and at the time assumed initially that it was to blame, when in fact it was as simple as the globe holders not working correctly.
Today I received from boyracer a genuine keyless remote, as I discovered the keyless controller behind the glovebox (again while trying to sort the foglights).
I followed the programming instructions on here and miata.net with no luck - the locks didn't cycle. I tried the process ignoring the "locks will cycle" step and the fob paired and was triggering the indicator flashes per normal... hmm.
Tried pairing the remote from the alarm the same way - no luck - there's probably some other way of doing that but I don't have a book!
So I cut it out.

Actually not too difficult, two ground connections (one in the footwell, one in the engine bay), 2 wires to the flashing LED indicating that it has an alarm, cut the wire running to the siren and put a bolt wrapped in tape in the grommet to keep the footwell sealed from the engine bay. Unplugged the alarm unit itself, and cut three wires running to the boot.
Tried again. Lights still flash, passenger door unlocks as factory (including re-lock timer) but the driver's door does not. Boot clicks but doesn't unlock when pushing the lock button. Passenger door locks when hitting the boot button.
Removed boot trim, the boot connector has been cut and intercepted with one of the three wires run from the front. Cut that off and soldered back to the original - boot now opens with the lock button. Ok, I can live with that (and resolve later) - but the driver's door not unlocking is a pain!
Operating the driver's lock manually or using the lever on the inside handle locks and unlocks both doors, so the wiring connector is ok.... but it's a five wire connector. Two of the alarm connectors dissapear into this loom, right up inside the kick panel. My hands aren't small, but on about the tenth go I manage to unwrap the loom and discover two connectors taped back into the loom. I determine after looking at the other side of the car that the wires are the door lock remote trigger wires. The two wires added are pulled out of the connector and these plugged in. Whoops. I had a 50/50 chance of getting them right way around, but now the driver's door does the opposite of the passenger door. More cramped work and a few minutes later and they're swapped around.
Bam. 3 hours later and I've got a working keyless remote system, no more alarm, although confusingly reversed boot/lock buttons on the remote. Anyone with any insight there would be very helpful; otherwise I'll work out how it's all wired and swap over the signal wires for boot vs car I guess... how are the lights supposed to flash? I don't remember from my last NB8B. I get two flashes for "unlock" which does as it says, one flash for "boot" which actually locks the car, and no flashes when I push "lock" (which opens the boot).
I think I'm also going to use the boot lid trigger pin as a number plate light switch same as NB8C have standard, perhaps not straight away, but eventually. It's handy that the battery is in the boot as I'll only need to run a relay, fuse, and power wire from the battery to the light loom, switched to ground with the boot pin.