Re-try refilling the autobox with ATF with the engine running and manipulating the gears. If this doesn't work hook up a diagnostic tool to the OBD2 port and check whether the gears and xyz switch is functioning OK which will read wxyz on the diag tool. IMO, my guess is the autobox oil pump is NOT being driven OK by the torque converter athough you left the TQ in place when removing and replacing the engine. It is possible to check the autobox for oil circulation and pressure I believe.

 

From the RAVE:
9. Fill gearbox with recommended oil to bottom of oil level/filler plug hole.
10. Select 'P' (Park).
11. Ensure handbrake is applied.
12. Start engine and allow it to idle.
13. Apply footbrake.
14. Move selector lever through all gear positions, while continuing to fill the gearbox. Select 'P' (Park).
15. With engine idling, continue filling gearbox until a 2 mm bead of oil runs from oil filler/level plug hole.
16. Fit new sealing washer to automatic gearbox filler/level plug, fit plug and tighten to 30 Nm (22 lbf.ft).
17. Stop engine.
18. Remove all traces of oil from gearbox casing.