1000cc JDMs are Vitz, Passo, Mirage, Suzuki XBee, some imported swift (most are 1200cc). Mentioning some that are imported here.
Passo/Vitz are the most common. Their parts are easily available, mechanics have understanding as well (but consult the manuals to ensure proper maintenance). They are non-turbo, and pretty robust. Passo has good mileage, specially the new ones, Vitz is good fun to drive.
I will recommend WagonR or Cultus or Picanto because despite being lower quality cars will be brand new, with warranty, and better overall in your case.
But do go for a good Vitz/Passo if you can find a good clean car.