Hi Adam
Welcome to our Forum :)
I don't would recommend you to do this.
I have the very big luck that I could buy a wrecked YRV GTti with the K3-VET engine. But this cars are very rare (only 150 pices in Germany AND Austria), did you got a K3-VET engine?
There is NO manual gearbox that will bare the torgue of the K3-VET engine.
There are more guy's in Singapore who want to do the same then you, but they all have the same problem that there is no manual gearbox who can handle the power from the k3-VET engine.
You can visit here at:
http://www.myyrvforum.com/forumv3/
One guy from Malaysia put a complete K3-VET engine with his automatic gearbox into a "Perodua Myvi" (lic. build from the actually Daihatsu Sirion /Daihatsu Boon) this works.
But your next problem is that you need a COMPLETE new electronic if you wan't to use the K3-VET EFI-ECU, this ECU is have a different wiring diagram AND he "speak" to the Automatic-ECU and to the "immobilizer-ECU", so the Automatic-ECU delivers some parameters to the EFI-ECU you really need, such as speed, actually gear from the automatic and much more.
The EFI-ECU of a YRV 1.3 TOP and the YRV GTti (K3-VET) is differnt in hardware.
Take a look at the attached pics. The darker picture show's you the (damaged) EFI-ECU from the K3-VET engine, the lighter one is from a K3-VE engine (YRV 87 HP). The EFI-ECU from your Sirion is only different in software to the K3-VE engine's EFI-ECU.
You did it better if you complete re-design your Sirion (K3-VE2 engine) with different pistons, different compression rate, put a Turbo on it and build your own engine's management Hardware for your new engine. Look to the upper right side and compare it....
I rebuild my YRV 1.3 TOP 87 HP manual transmission to a K3-VET fittet YRV WITH Automatic gearbox.
It is a VERY hard job to do what you want to do.....
Greetings
Rainer