That's the big difference between the earlier MEMS1.9 and the later MEMS3 equipped cars, you're right Ali. Then there are differences to a variety of parts and sensors depending on which car the engine was originally fitted to.
The basic block and head castings are all the same* (*actually, there are detail differences, but none that will prevent you fitting a K16 engine from one car to another). It's the ancillaries, sensors and HT system that will differ.
In my opinion, now you have the "good" replacement engine, is to strip the original down, and swap all the ancillaries (alternator etc), sensors and the cam cover (if it is different) to the "new" engine.
One hurdle to be aware of is that the older MEMS1.9 engine use a different exhaust cam, which does not have the reluctor ring fitted for the cam position sensor. If this is the case, you'll need to swap the cams over too (a minimum of the exhaust cam if going MEM1.9 to MEMS3, or the inlet cam with the distributor drive spigot if going from MEMS3 to MEMS1.9).
