The somewhat cyclical idle seems to be an irritating trait of these engines. On my Metro it seems to be related either to engine temperature or astrology, the phases of the moon and voodoo... I think it's engine temp, but I am willing to entertain other ideas!
At any rate, have you done the typical maintenance these engines need-namely de-carboning and a good compression test? Have you put in a fresh PCV valve and cleaned out the system? Are the vacuum hoses all new? I may have missed it but if you are using a used engine and not a rebuilt one you likely need to catch up it's maintenance as most Metros have seen very hard lives. Also, three cylinders are inherently unbalanced engines and tend to vibrate more than engines with even numbers of cylinders. This trait can be lessened with a balance shaft, but the G10 uses no such device. This is why it is important to use the stock circular motor mounts to absorb most of these vibrations. Otherwise, the steering wheel will be like holding on to a jackhammer.
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No green technology will ever make a substantive environmental impact until it is economically viable for most people to use it. This must be from a reduction in net cost of the new technology, not an increase in the cost of the old technology through taxation
(Note: the car sees 100% city driving and is EPA rated at 37 mpg city)