On the diagnostic plug in the passenger fot area there are only a few pins that are important for basic engine diagnostic:
All that's really needed is pin 4, 16 and 7.
4 and 16 are obvious 
7 is connected to the ECU, which in the case of the Honda ECU would be E23
If this is connected then an engine diagnostic tester would be able to connect to the Honda ECU and check it's status for emission stuff.
On an S2 Elise this is a simple operation as the wires from the diagnostic plug go directly to the back of the car and to the original ECU connector and all you need to do is move 1 wire. These cars do not have a transponder key system like the Speedster but use a separate immobiliser that's integrated into the alarm system.
On the Speedster this is done differently..
The original Opel/GM ECU in the back is/was connected to an immobiliser with antenna ring around the ignition lock. In your original key there is a transponder chip and if you try to start the car the immobiliser will check the key and send an 'OK' signal to the ECU to start the engine if the transponder chip inside the key is recognised.
Because you do not want thieves to install a new immobiliser in the car, both the immobiliser and the ECU are 'paired' to each other with a (secret) PIN code so you can't just replace the immobiliser to start the car with a fake key.
To make this system secure they also use the immobiliser as a 'message passing' box that sits between the diagnostic plug and the ECU and will only relay data between the diagnostig plug and the ECU if they are 'paired' properly (so you also can not re-program keys with a replacement immobiliser fitted..).
This is why normally you need to 'unlock' or 'de-pair' the ECU and immobiliser before installing a new ECU or immobiliser in these cars.
Now...
In your setup with the Honda engine and ECU the original GM/Opel immobiliser and transponder ring on the ignition lock will be useless.
The Honda ECU can not talk to the Opel/GM immobiliser to get a 'go or no-go' handshake (these protocols are proprietary and vendor specific) and it will have no function. You should be able to start the car normally if you have for instance a key copied without the transponder and try to use it. In your case it should start quite happily once you turn the key press the start button. With the Opel/GM engine/ECU it would start and then cut out in about 2 seconds.
Check the path of the wiring from OBD pin 7 to the ECU in the schematics and you should be able to see what's going on.
BTW.. The original META alarm system on the Speedster is completely separate from the engine and ECU and does not do anything to prevent the car from being started. It just makes noise.. Nothing else.. It could be set up to work as an immobiliser like in the Elise but you need a few extra parts. (unless your car already has a different/aftermarket alarm system.. that could include an immobiliser setup inside it..)
But to get the Honda ECU diagnostic information on the OBD plug (which is what you want) you will need to make some changes:
Either:
- Keep the existing wiring in place and bypass the original immobiliser from the data path and then pick up the signal wire in the back of the car and connect it to the Honda ECU so the Honda ECU E23 is wired directly to OBD pin 7, 'skipping' the immobiliser.
Or:
- Run a completely new wire from the OBD plug to the honda ECU and crimp/solder/wire to the OBD plug pin 7 and Honda ECU pin E23
or:
- Buy a new OBD plug and just install/connect pins 4, 16 and 7 and wire these to GND, permanent 12V and Honda ECU E23 and push the original diagnostic plug away and tell the guys to connect to this one for their checks.
In the last option you may want to keep the original plug in place as this also provides access to the ABS and Airbag/SRS system if you ever have problems/errors there.
Bye, Arno.
