Go for proper rebuild, from some good and competent mechanic; who gives warranty of at least 40~60,000 Kms of his work, uses genuine, OEM parts in brand new condition, and rebuilds as per company specs.
As far as I know, most parts of 1KR-FE 1000 cc Vitz engine are available in brand new condition.
Swapping should be the last choice.
I hope, all above helps and guides. Thank you.