Do check gear box oil pump bearing. Actually i bought gear for my 1KR-FE. The engine from which the gearbox was opened was in pristine condition but its oil pump bearing was bad (whizzing sound after driving car for about 2 3 KM) and like after running for a day or two the gear refused to change ratios it would just stick to one ratio. Took the car back gearbox was found to be faulty. Got replaced by another kabli one and its working like a charm.
Do open up the chamber of gearbox and check for dents. The chamber have some magnets and while transporting the chamber may have get some dents which would displace the magnets and might affect the transmission. My one had some dents so also got that replaced.
Note: 1300cc (2SZ-FE) and 1000cc(1KR-FE) share same gearbox. Am currently using one opened from 2SZ-FE with 1KR-FE.