Wow. That is a really good deal you got there. All those bits for 150 quid is excellent. Well done.
Yes, the rfid transponder is in the top [grip] part of the key. You get a really sharp scalpel and (carefully) cut the rubber part parallel to the table-top (if you imagine the key lying on the table) from the corner. Parallel to the key blade, if you wish, there is even a molding "seam" you can sometimes see) . It is impossible to tell you which side (left or right of the key-fob hole) as the key looks the same from either side. Google PCF7936 to see what you are looking for in the key (or open up the wee plastic key if your bike came with it). The transponder is housed in a little plastic holder inside the molded rubber and It is much easier to put it int the plastic key for a test, if you need to). Treat it carefully. if you lose or damage it, you are back where you started.
Your original ECU will store the Bike's VIN number, options as added at the factory, mileage and information about past faults, the adaptations and the key data. These will all be wrong with the new ECU, obviously, as they are from a donor bike. Swapping the rfid transponder into your original key will leave the original locks on the bike, which is fine. If the spec is exactly the same on the bikes (i.e. ESA, ABS, alarm, etc.) then you won't need re-coding [Well, the mileage will flash all the time because it is a mismatch with the KOMBI (clocks), but that won't stop you running the bike. That is why I was asking about the clocks. (Unless, if you were that lucky that the mileage is within a couple of hundred miles)]
@Santa, Yes, agreed, that would work perfectly fine, mate. The key transponder is the same, the metal bit is relatively easy to copy.
As we are "chewin' the fat" on the topic... There is another [really bad] idea you can do. You can take the RFID chip from the working key and permanently glue it to the ring antenna. That way you downgrade your security to about 1974-level

where the immobiliser is always seeing things as "A-ok" and you are relying only on the mechanical part of your keys for security. People do this to keep their original keys (says t'Internet, anyways) This is a really bad idea. Don't do this, unless you have to get yourself home [from middle of Gobi desert] as an emergency. You are essentially "deleting" your immobiliser.
Now, Having written all this... I am thinking we should probably ask the mods to trash this topic once you've solved the problem, Glenn.1 . There is way too much info here that can be used to help scrotes steal bikes. (Or am I being naive here and everyone knows all this?) All this info is already available on the net anyways, but took me a long while to put together... why make it easier...
Cheers.