Yar, if engine is running fine, I mean, if starting is okay, accelerates good and if yr mech says it's a good engine then better change its throttle body. Just replace the old one with efi throttle system. By doing so many other items will be changed and a few additional things will be required.
2nd option is that change it with same Daihatsu engine or vitz 1000cc 1KR engine.
I kept a Coure for more than 9 years and overheated it thrice and changed the gas kit only the last time as it needed to be changed.
So, in my opinion and experience Coure's 847cc engine is a badass engine. Don't lose it. If there is any minor issue then try to fix it 1st and if not fixed then go for other options.